In the late 19th century, amid attempts to apply science to notions of race, some advocates of Zionism sought to reformulate conceptions of Jewishness in terms of racial identity and the "race science" of the time. They believed that this concept would allow them to build a new framework for collective Jewish identity, and thought that biology might provide "proof" for the "ethnonational myth of common descent" from the biblical land of Israel. Countering antisemitic claims that Jews were both aliens and a racially inferior people who needed to be segregated or expelled, these Zionists drew on and appropriated elements from various race theories, to argue that only a Jewish national home could enable the physical regeneration of the Jewish people and a renaissance of pride in their ancient cultural traditions.

The contrasting assimilationist viewpoint was that Jewishness consisted in an attachment to Judaism as a religion and culture. Both the orthodox and liberal establishments, for different reasons, often rejected this idea. Subsequently, Zionist and non-Zionist Jews vigorously debated aspects of this proposition in terms of the merits or otherwise of diaspora life. While Zionism embarked on its project of social engineering in Mandatory Palestine, ethnonationalist politics on the European continent strengthened and, by the 1930s, some German Jews, acting defensively, asserted Jewish collective rights by redefining Jews as a race after Nazism rose to power. The advent of World War II led to the implementation of the Holocaust's policies of genocidal ethnic cleansing, which, by war's end, had utterly discredited race as the lethal product of pseudoscience.

With the establishment of Israel in 1948, the "ingathering of the exiles", and the Law of Return, the question of Jewish origins and biological unity came to assume particular importance during early nation building. Conscious of this, Israeli medical researchers and geneticists were careful to avoid any language that might resonate with racial ideas. Themes of "blood logic" or "race" have nevertheless been described as a recurrent feature of modern Jewish thought in both scholarship and popular belief. Despite this, many aspects of the role of race in the formation of Zionist concepts of a Jewish identity were rarely addressed until recently.

Questions of how political narratives impact the work of population genetics, and its connection to race, have a particular significance in Jewish history and culture. Genetic studies on the origins of modern Jews have been criticized as "being designed or interpreted in the framework of a 'Zionist narrative'" and as an essentialist approach to biology in a similar manner to criticism of the interpretation of archaeological science in the region. According to Israeli historian of science Nurit Kirsh and Israeli geneticist Raphael Falk, the interpretation of the genetic data has been unconsciously influenced by Zionism and anti-Zionism. Falk wrote that every generation has witnessed efforts by both Zionist and non-Zionist Jews to seek a link between national and biological aspects of Jewish identity.

Though the question is undecided, some trace the start of a biological interpretation of Jewish origins back as far as the Spanish Inquisition. A tradition of thought and ethnography premised on a hierarchy of racial distinctions, though in retrospect known to be a pseudoscience, was deeply entrenched, indeed ubiquitous, among Western scholars by the early twentieth century. It saturated thinking in medicine and anthropology, but assumed particular prominence in the Germanic sphere as opposed to England where, John Efron writes, "Jews as Jews simply failed to arouse British scientific curiosity". As participants in modernity, Jewish thinkers and scientists formed an integral part of the scientific world underwriting these theories. The Nazi Holocaust totally discredited concepts of race and, from 1945 onwards, considerable efforts were made to disabuse the world of the prejudicial notion that Jews constituted a race. At the same time, the broader thrust and impact of this discredited world-view long remained insufficiently analysed.

Ethnic origins have figured as an indispensable basis for determining what groups belong to the Jewish collective. Admixture by conversion tended to be underplayed in traditional Jewish historiography in contrast to speculations about descendant communities from the biblical Ten Lost Tribes who in theory would belong to the Jewish "blood community". When Arthur Koestler's The Thirteenth Tribe (1976) propounded the thesis that the origins of the Ashkenazi might be found in the dispersion of the Turkic Khazars, the book encountered a mixed reception within the Jewish American community, which was increasingly adopting Zionism narratives during this time period, and a hostile reception from American Zionists, who condemned the work as "a product of Jewish self-hatred". Though the book's genetic implications are not regarded as tenable, this severity of critical dismissal, according to Elise Burton, reflected an inability or unwillingness to take cognisance of a tradition of a racializing logic in Zionist discussions of a putative Jewish biology. Though as early as 1967 George Mosse had alluded to the striking similarities between Zionist discourse on race and those made by their völkisch German ethnonationalist antagonists, the academic mainstream tended to treat it as a taboo.

In 1983 the historian Joachim Doron (1923–1993) examined the tradition of acerbic attacks Zionists once mounted against Jews of the diaspora, much of which concerned differing ways of interpreting Jews as a nation/race. Many aspects of the role of race in the formation of Zionist concepts of a Jewish identity were rarely addressed, sidelined or deliberately suppressed until recent decades. Doron suggested four reasons for this silence. Firstly, these scathing polemical recriminations by Zionists against other Jews, "the enemy within", overlapped with anti-Semitic arguments about Jews, and recalling them would only play into the hands of modern anti-Semites. Secondly, both Holocaust survivors and veteran settlers had begun to feel nostalgic about the lost world of the shtetl, whose idealization led them to ignore negative characterizations of life in the Pale in the 19th–20th century Jewish/Zionist tradition. Thirdly, as a young nation forging a new Jewish identity with ramifications for the postwar diaspora, a vision emphasizing whatever was positive came to dominate Jewish history in Israel. Finally, the country's growing political isolation encouraged a trend to ignore world opinion, in Ben-Gurion's words, to disregard "what the goyim say". Jewish issues that an earlier Zionist press would have excoriated as "scandalous" came to be dismissed as just expressions of Jewish self-hatred.

Beginning in the 1990s this topical neglect has been gradually addressed in detail, beginning with a German monograph by Annegret Kiefer in 1991, and, in English, John Efron's landmark study, Defenders of the Race (1994). Brief notices emerged occasionally hinting at gaps in the record. Mark Gelber, in an aside on his chapter on Nathan Birnbaum, whose racialist ideas had a seminal impact on Cultural Zionism, remarked in 2000 that the "racialist orientation" of Birnbaum's student Martin Buber had been "relativized or sometimes even suppressed in scholarly literature and other commentary about him". In the same year Mitchell Hart, on the heels of his 1999 essay, explored these themes in terms of social science in a book-length study. Many studies began to fill the lacuna, by examining the racial thinking embedded in the national ideology constructed around Jews in its formative period. By 2013, Doron Avraham noted that a number of studies had explored Jews' self-"racialization" in relation to the fin-de-siècle period, although later periods remained less researched.

Some of this scholarship made connections between earlier Zionist understanding of race and more recent genetic debates in Israel. Nurit Kirsh wrote in 2004 that investigations into the biology of the Jews had rarely been explored for two decades after the state's establishment, and argued that Zionist ideology had been so internalized by scientists that the myths remained as unconscious influences on their approach to the subject of population genetics. The following year a special issue of Jewish History dedicated several articles to aspects of the topic of Jews and racial classifications, and Tudor Parfitt published his study of the interrelation between genetics and Jewish identity among the Lemba and Bene Israel.

The Israel geneticist and historian of science Raphael Falk argued that explicit racial and eugenic notions linking Jewish nationality and biology were particularly in evidence among Zionist writers, but also among non-Zionists, and have continued, "though in a thinly disguised mode", after the defeat of Nazism to resurface in every generation since. For him "the utilisation of biological arguments as 'evidence' for whatever social, economic, or political notion that has been put forward" remains problematic. Falk comments that he knows of no other example of an ethnic conflict where this effort to prove or disprove the biological belonging of modern Jews to the historical Land of Israel played such a role.

Historian Steven Weitzman writes that postwar genetics worked to distance itself from race science for both scientific and ethical reasons. Weizmann documents the significant and profound differences between genetics and race science, while noting intellectual similarities. He concludes that some insecurity about the ambiguities of Jewish identity, inflected by social, psychological and political concerns runs through the centuries-long scholarly quest for Jewish origins even to the present. The mystery continues to attract attention, he says, but cannot be solved by scholarship. Attempts to do so, to ground an alternative "creation myth" in scholarship, prove to be tendentious or deleterious.

According to Elise Burton, "Historians and anthropologists have critically examined how the structuring assumptions of Jewish race science in early-twentieth-century Europe and North America, and their relationship to Zionist nationalism, reverberate within the genetic studies of Jewish populations by Israeli scientists from the 1950s to the present." Genetic studies on the origins of modern Jews have been criticized as "being designed or interpreted in the framework of a "Zionist narrative", as essentializing biology, or both" in a similar manner to criticism of the interpretation of archaeological science in the region. According to Kirsh and Falk, the interpretation of the genetic data has been unconsciously influenced by Zionism and Anti-Zionism.

Noah Tamarkin, assistant professor of Anthropology and Science and Technology studies at Cornell University, in reviewing the literature, writes:

Contemporary geneticists and their critics often consider similar questions and controversies such as those raised in pre-1980s studies based on blood groups, and even earlier biometric studies undertaken by 19th- and early-20th-century eugenicists and their critics. Zionist and anti-Zionist politics significantly inform historical and contemporary Jewish genetics literatures, at times explicitly and more often implicitly in the questions that scholars ask, such as the extent to which Jews constitute a biological community, and the extent to which Jews throughout the world can trace their ancestry to the Middle East.

Traditional Christian Judaeophobia was tempered under the impact of the Age of Enlightenment as a succeeding period of Jewish emancipation in Western civil society took root in the 19th century. Many acculturated Jewish communities integrated into Germanic society, came to consider their Jewishness in terms of their cultural and/or religious heritage. Coinciding with the emergence of Darwinism as a biological science of man and the rise of scientific racism more broadly, the Emancipation period's incremental lowering of traditional socio-cultural discrimination against, and persecution of, Jews faced new challenges. Though there was no intrinsic connection between Darwin's theories and antisemitism, the latter half of the 19th century witnessed the rise of a racial antisemitism (Wilhelm Marr 1873, 1879; Eugen Dühring 1881, for example) which often had scientific pretensions.

In the German cultural world in particular, this retuning of nationalist völkisch thought drew strength from the "biologization" of human differences in the form of theories of organic racial typologies, by seeking an ostensible scientific support in social Darwinism's theory of evolution as a struggle between species. Jewish scholars and scientists were therefore forced to confront the new race science and, in the words of Todd Endelman, "[s]ome disputed the stability and permanence of racial traits and the existence of pure races. Others internalized racial thinking and then unconsciously reworked and subverted its premises. Still others accepted the idea of racial differences but turned conventional stereotypes on their head."

Jewish scientists who espoused assimilation and accepted the broad parameters of the racial paradigm tended to rethink race in terms of Lamarckism, which allowed that environmental factors could modify an inherited genetic makeup. Zionist scientists, contrariwise, were often convinced that the supposed defects of the "Jewish body" were a direct consequence of integration into other societies, and were drawn to an essentialist interpretation of race. For the former, race was a flexible reality amenable to improvement while the latter thought traits engendered by Mendelian principles involved a more rigid scheme of biological determinism. For instance, when the assimilationist Joseph Jacobs' "anthropometric research" (i.e., phrenology) suggested in the 1890s that Jews were "brachycephalic," the problem arose as to how to reconcile that apparent result with race scientists' belief that Arabs and Sephardim, as Semites, were "dolichocephalic," if all Jews descended from a Semitic "race"? One implication was that Jews were thereby not "pure" but the product of racial intermixture. The other possibility was that environment factors could modify physical traits.

As the older Christian antisemitic prejudices were reformulated in an age of racialised thinking, some Jews, disappointed with what they perceived to be the failures of full emancipation, began to be drawn to Theodor Herzl's proposed Zionist solution to the quandary. Herzl's Zionism arose in reaction to these renewed antisemitic trends, as an ideology that aimed to reconstruct a distinct Jewish identity along "ethnic"/"volkisch" lines. In doing so, Herzl and his followers challenged the centuries-old tradition among assimilated Jews that they constituted a religious and socio-cultural group by reframing Jewishness in terms of the concept of a nation-race, with Jews conceived of as an "integral biological entity" in what has been called a "racialization of Jewish identity". Purity of race became a paramount theme of Jewish anthropology. Biological considerations shaped Herzl's own outlook. He likened the Jews of his day to seals, thrown by circumstance into water but, once back on ground, they would refind their legs, and antisemitism itself, a shock treatment, might prove functional in this restoration of Jews to their former selves.

Zionist physicians and scientists varied notably in the way they used race to illustrate any number of social, economic, or political notions. According to Dafna Hirsch of the Open University of Israel, writing in 2009, many Zionists supported the concept of Jews as a race, often believing it "offered scientific 'proof' of the ethno-nationalist myth of common descent", while others used it to emphasise diversity and hierarchy within the Jewish people. The variation of Zionist positions on race has been observed by Todd Endelman in a study of Redcliffe Nathan Salaman, Shneor Zalman Bychowski and Fritz Shimon Bodenheimer who drew on race. The debates over race swung between the two poles, and covered multiple shadings, of a complex typology that opposed two stereotypical kinds of Jewries, the emancipated, modern cravatte (assimilated) Jews of the German cultural sphere and the religiously fervent, trading caftan Jew (Ostjuden), and played a notable role in the arguments that broke out between Zionists and assimilating Jews. Herzl himself dismissed assimilationists who opposed him as "Mauschel", who perhaps were not fully Jewish because of some past miscegenation.

In the early years of the Zionist movement, notable proponents of the idea of a Jewish nation-race included Max Nordau, Herzl's co-founder of the original Zionist Organization, Nathan Birnbaum, one of the founders of Central European Zionism, Arthur Ruppin, and Ze'ev Jabotinsky, the founder of Revisionist Zionism, Nordau, a theorist of muscular Judaism and devoted follower of the theories of Lombroso, wrote that "(t)he acute eye of the street loafer is sufficient proof that the Jews are a race, or at least a variety, or, if you please, a sub-variety of mankind", a common view advanced by one of the founders of physical anthropology, Johann Friedrich Blumenbach. Birnbaum, though he militated against a latent trend in Jewish nationalism that "craved to answer antisemitic nationalist chauvinism in kind", still thought race was the foundation of nationality, Jabotinsky wrote that Jewish national integrity relies on "racial purity", that "(t)he feeling of national self-identity is ingrained in the man's 'blood', in his physical-racial type, and only in it."

From 1908 to 1942, Arthur Ruppin, considered the "father of Israeli sociology", played a central role as director of the Palestine Office (PO) and core organizer of Zionist 'colonization' in all of its dimensions from land purchase and banking to settlement policies, education, the establishment of modern Hebrew and the construction of a new Jewish-Zionist identity (Bildung). Ruppin often quoted approvingly from the writings of the foremost Nazi scholars and scientists, and in 1933 met for a discussion Hans F. K. Günther, Heinrich Himmler's mentor, and Germany's highest authority on racial theory, a figure later caricatured as Nazism's Rassenpapst (race-pope).

For Ruppin, what Zionism required was to weed out inferior, "semitic" racial elements among Ostjuden and select only those whose biology was best adapted to the soil and climate of Palestine where, by productive agriculture and militarization, they would vindicate their racial affinity with biblical Hebrews. To that end he drew up a hierarchy of Jewish racial types which distinguished Ashkenazi – allegedly not Semitic but an Aryan breed via descent from Hittites and Amorites – from the inferior, presumptively Bedouin-related Sephardim. The positive qualities of the exemplary Urjude (archetypal Jew), once considered Sephardic, were transferred to the Ashkenazi while the negative stereotypes of Jews, mercenary and materialistic, were shifted onto Sephardim and Mizrachi Jews. As early as 1934 he successfully thwarted the implementation of a proposal by Yaakov Faitlovitch to bring Ethiopian Jews to Palestine on the grounds that they were "niggers" converted by the sword in 2600 BCE.

While there were other experiments in social engineering of the Jews, Bloom argues that only the Palestinian-Zionist initiative succeeded in its project, that of radically recasting modern Jewish identity and the "Jewish body". Ruppin, who used a Prussian model in settlement planning, played a major role in implementing the plan in practical terms. Deeply interested in racial hygiene (Rassenhygiene), with Otto Heinrich Warburg, Ruppin controlled most of the financial resources for immigration, and pressed for the selection of only the fittest Ashkenazi Ostjuden as olim for the "human material" of a "gene pool" of a new Jewish, non-Semitic Maccabean type. He did everything possible to dilute what he thought of as the deleterious dominance of the Sephardic/Mizrachi communities, who often depended on diaspora charity for survival, and restore the "germplasm" of the pure race of ancient Jews he considered dormant in the Ashkenazi. The strict eugenic policies meant that towards the end of the Second Aliyah (1912–1914) 80% of aspiring immigrants were rejected. The unfit masses of Eastern European Jewish refugees were deemed people best relocated in the United States.

In the 1930s, German Jews caught in the exacting tensions between the hammer of exclusionist antisemitic race policies under Nazism, and the anvil of total assimilation, increasingly strove to redefine themselves in terms of the new hegemonic discourse of race, appropriating the language of their oppressors in order to subvert its implications of inferiority.

These matters and discussions were not widely disseminated in the Jewish population before the 1930s. Not all Zionists using concepts such as "race" at this time agreed on its biological dimension. Some Zionists – for example Robert Weltsch and Israel Zangwill – did not embrace the racial idea. Cultural Zionists such as Ahad Ha'am, Martin Buber and Theodor Lessing emphasised the cultural or spiritual decay of the Jewish people rather than its biological or racial decay, echoing wider cultural discourses around decay and degeneration in European culture of the time – but sometimes used biological metaphors. For example, according to Robert Weltsch at the time, an orientation towards race had been foreshadowed in Buber's Three Addresses on Judaism (1911) where Buber spoke of blood determining thought in the deepest layer of power in the soul which dictates every tone and every colour of Jewish existence. Other Zionists harshly criticised race science, preferring a conception of Jewish religious heritage to one of descent. On the other hand, even some non-Zionist Jews began to understand Jews in racial terms in this period.

The effect of Nazism and its genocidal policies discredited racial science and "postwar genetics worked hard to distance itself from race science for both scientific and ethical reasons". In a four-point Unesco declaration in 1950, any correlation between national/religious groups and race was denied, and it was affirmed that race itself was "less a biological fact than a social myth". According to the Israeli historian of science, Snait B. Gissis, an emotional barrier caused Israeli geneticists and medical researchers from 1946 to 2003 to take pains to avoid the term "race" in their scientific publications. The use of race still lingered on, nonetheless, in the anthropological literature, and highly influential geneticists such as Leslie Dunn and Theodosius Dobzhansky, who had been critics of race science, persisted in maintaining that races did exist, and substituted "race" by "populations".

In the decade after 1948 Israel underwent massive immigration with 70% of Israeli Jews having been born elsewhere. The marked heterogeneity of these disparate peoples, according to Raphael Patai, generated at the time serious interethnic friction among Israeli Jews, while at the same time making the very idea of a "Jewish race" seem a myth. It also shifted, according to Falk, the earlier emphasis on healing the ostensible "degenerative" blemishes, hereditary or environmental, of Jewish bodies and souls which Zionism imputed to life in the diaspora, towards investigating the nature of hereditary diseases found in the incoming communities. The groups in this influx were classified in terms of edot , "communities", or ethnic subgroups and constituted a very heterogeneous society. Often striking differences in inherited diseases within these edot emerged as population genetics began to examine this new aliyah wave's Jewish communities. Numerous Israeli biologists were excited by the research opportunities afforded by the new demographic situation in this "special historical moment". One offshoot of this intense focus on the genetics of hereditary disease was to explore also the phylogenetic relations between these edot and determine their origins, a focus influenced by political interests. In reviewing the literature of this period, Nurit Kirsh concluded that, though working within the framework of international science, the approaches adopted by Israeli geneticists at the time were "substantially affected by Zionist ideology", with its notion that Jews were a non-European race whose purity was conserved despite millennia in diaspora.

A standard approach adopted by Israeli geneticists traditionally was to privilege research on gene frequencies among Mizrachi and Sephardi groups as opposed to Jewish communities of European background. The overall 19th century assumption that Jews were a pure isolate, nonetheless, still remained in force, a premise shared by scientists abroad, who also embraced the idea in the decades from 1950 down to the 1970s that Jews had little admixture, and constituted a genetic isolate, a position Israeli scientists promoted among their colleagues abroad.

From the 1950s down to the 1970s, when they gained momentum, two trends emerged in human genetics research. On the one hand, studies of racial admixture intensified, while statistical models grew more sophisticated, particularly as computer programming allowed for greater complexity in calculations of genetic distance to establish how close otherwise distinct communities might be. Such distances, visualized in dendrograms, are based on variations in gene (allele) frequency between groups under comparison. Israeli geneticists, who had been accustomed to consider diasporic admixture an irrelevancy as they strove to reconstruct an ancient Jewish gene pool, worked closely with the prominent Stanford school headed by Luca Luigi Cavalli-Sforza, Walter Bodmer and Samuel Karlin. From the early 1970s, research on HLA gene frequencies among Israel's ethnic subgroups targeted Mizrachi/Sephardim communities, but also examined blood from non-Jewish Israeli citizens, such as Armenians, Druze and Palestinians.

In the mid-70s, a growing sense of crisis compounded anxieties among Israel's dominant class as the Mizrachi began to challenge the cultural, social and political ascendency of the Ashkenazi elite, a challenge which was to culminate in the victory of Menachem Begin's Likud party in the 1977 Israeli legislative election. This internal worry was aggravated by the near simultaneous publication of books by two Hungarian Zionists, Raphael and Jennifer Patai's Myth of the Jewish Race (1975) and Arthur Koestler's The Thirteenth Tribe (1976). Both bestsellers showcased arguments for the importance of admixture in the formation of the Jewish people. While Patai provided extensive historical details of conversion and Jewish endogamy, his daughter Jennifer Wing, using a computerized equation by Cavalli-Sforza, concluded that the genetic distance between East European Jews and non-Jews was lower than that between Ashkenazim and Sephardim/Mizrachis. Though one purpose of these works was to cut the ground from under the feet of antisemites by revealing the fallacies of a "Jewish race" which underwrote modern hatred of Jews, the two publications increased anxieties among Ashkenazis both abroad and in Israel, who were privately disturbed by Likud's landslide ascendancy. Coinciding with these events, Elise Burton argues, geneticists began to scale down their Mizrachi fieldwork's importance and focus increasingly on analyses of data sets in an attempt to rebut the Patai/Koestler thesis of admixtures of Jews and non-Jews and locate the Ashkenazi within an Eastern Mediterranean setting.

In responses that challenged Patai's claims, two analytical teams, one led by Dorit Carmelli and Cavalli-Sforza, the other headed by Bonné-Tamir, Bodmer and Karlin, developed two different statistical models to evaluate the genetics of common Jewish origins, dispersion, drift and admixture. While they shared similar assumptions about the defect of Patai's analysis of admixture, their own distinct methods generated different quantitative results and interpretations, laying the seeds for a future controversy about admixture. At a presentation in 1977, the Israeli team outlined their work showing no significant admixture from Europeans in "Mediterranean" Ashkenazis. Cavalli-Sforza's calculations by contrast suggested little admixture in Mizrachi Maghrebi, Iraqi and Iranian Jews as opposed to almost 54% of admixture in the Ashkenazi. However, if data from HLA gene frequencies was added, Ashkenazi appeared to have no admixture. It followed for Cavallo-Sforza that any attempt to determine admixture from non-Jews in Ashkenazis was premature. In 1978 Karlin then developed a new statistical model for genetic distance calculations, which, applied to the data, suggested Ashkenazim were closer to Jewish and other Middle Eastern populations than they were to Europeans. Genetic inflow from non-Jews was deemed minuscule, and until 1984 this became the consensus view of Israeli geneticists, who considered the problem solved, and rarely mentioned the differing results obtained by the Cavalli-Sforzi-Carmelli approach, though in 1980 Newton Morton, detecting serious flaws in Karlin's statistical analysis, had strongly criticized the objectivity of the Israeli consensus verdict. Thereafter, however, Israeli biologists returned to the study of Mizrachi groups, several of whom were acknowledged to have higher admixture.

Morton's distinctive modeling backed the Patais' admixture theory by yielding an average 1% of gentile admixture per generation, and therefore lent support to Cavalli-Sforza's earlier conclusion. Cavalli-Sforza commented that, depending on the genetic markers selected, vast discrepancies in admixture estimates could be generated, and therefore no adequate statistical model was yet available to determine the ratios of admixture. In Burton's interpretation, both approaches were guilty of circular reasoning, with a 'known' version of Jewish history influencing the design of the very statistical formulae ostensibly crafted to ascertain it. in 1986 Ranajit Chakraborty, in a lengthy paper on the statistical methods used to determine degrees of genetic admixture in human groups, cited the genetic literature on the Ashkenazi as one of the three cases in population genetics where researchers produced discordant conclusions, the other two being African Americans and Icelanders. In 1991, Roselle Tekiner, commenting on Zionism's aim to forge an inclusive Jewish identity from the "ingathering of the exiles", argued that attempts to create a single identity out of disparate Jewish populations had failed. One 1974 study showed that a significant minority of Israelis lacked a sense of identity with the wider world of diaspora Jews. The growing secular constituency required more than the consensual view, grounded in a theological right to the land, to connect into a generic Jewish identity. Tekiner suggested that Zionist tacticians and others, nonplussed by this failure, might look for scientific proof to convince secularists in particular that they formed a part of a biologically integral 'race' descended from the biblical Hebrews.

In Elise Burton's summation, the infra-academic conflict above, which led to divergent results between the two schools, reflected different foci of interest for the respective research teams. The Israeli school specialized in Jewish and Middle Eastern populations, whereas the primary aim of the group around Cavalli-Sforza directed its project towards a much broader, global problem, that of the genetic history of all migrating human communities. The latter considered that the intricate history of Jewish populations across the diaspora was far too complicated for the purpose of testing admixtures.

By the early 2000s, studies on the Zionist racial narrative gave way to modern genetic research, which was often met with controversy. Critics saw this new research as recycling earlier discredited metaphors of blood and race, repackaged as the biological variation between ethnic populations.

DNA sequencing from the 70s onwards had been slow even as it became a widespread analytical tool for positions in the debate on Ashkenazi origins. With the rise of automatic whole genome sequencing in the 1990s, research took rapid strides but controversy has remained an ongoing problem. Susan Martha Kahn in a 2005 overview of work on Jewish genetics observed that "racial assumptions about Jewish genetic uniqueness" were still a contemporary issue. At the end of the decade (2011) Mitchell Hart stated that "race" still remained a notable feature of both scholarly and popular Jewish thought informing the construction of modern Jewish concepts of identity.

In 2012, two important books appeared providing different overviews of results and approaching the subject from seemingly antithetical positions, while drawing on the same data sets: Harry Ostrer's A Genetic History of the Jewish People, and Nadia Abu El-Haj's The Genealogical Science: The Search for Jewish Origins and the Politics of Epistemology. Ostrer outlined a trajectory arching over a century of studies on Jews, from Maurice Fishberg's The Jews: A Study of Race and Environment (1911) onwards. The scope of research showed a direct continuity, the difference lying in the great technical strides made since the early 20th century when the seeds were laid for modern genetics by the theory, which Fishberg's New York contemporary Thomas Hunt Morgan was developing, that chromosomal factors played a role in inheritance. Heirs to this tradition, Ostrer believed his generation was now in a position to apply sophisticated scientific methods to obtain a genetic answer to the crux of Jewish origins and identity. The result is, for Ostrer, that,"Jewishness can be characterized at the genetic level as a tapestry, in which the threads are represented as shared segments of DNA". Ostrer's research in contemporary molecular genetics advances a solution aligning traditional Jewish narratives with a biologically recognizable marker for Jewishness.

El-Haj, an anthropologist working within the field of social science examining genomic research, challenged Ostrer's conclusions. She considers the whole enterprise of using genetics to confirm a narrative of origins problematic. She cites the Israeli geneticist Raphael Falk for the view that while Y-chromosome markers are "signatures" indexing ancient origins, they do not constitute evidence of the biological unity of Jews. Her reading constituency, Kahn argues, also includes those anti-Zionists who would call into question a "foundational assumption on which the Zionist enterprise is predicated", and feed into the "discursive do-si-do of opposing narratives that characterize the ongoing Israel/Palestine conflict".

According to El-Haj and Burton, Jewish geneticists had to reconcile professional commitment to objectivity with their own personal investment in the topic. Tensions over objectivity resurfaced among Jewish scholars, and in Israel the Ashkenazi background of most scientists conducting gene research led to claims that they were predominantly focused on their own communities. Because these Jewish genetic researchers constructed historical narratives along with pure science, entanglement could provoke heated political impacts.

In overviews of the subject, both the geneticist Raphael Falk and the historian Steven Weitzman have written of the dangers of confirmation bias. Falk writes:

the history of the relationship of Zionism and scientific biology, which has made an effort to single out Jews from non-Jews on the one hand, and to unite the distinct Jewish communities on the other hand, provides a problematic case of the utilisation of biological arguments as "evidence" for whatever social, economic, or political notion that has been put forward.

Weitzman recognizes the problem, but argues that notwithstanding the suspicious impression given by many genetic studies that science is being used to endorse a traditional belief, in the Jewish case, there appears to be evidence that would point towards precisely such an overlap between belief and scientific research:

For some scholars, it is suspicious that genetic analysis would seem to be reaffirming what many Jews already believe about their origin. Sometimes, what the evidence reveals is that the actual biogenetic ancestry of people can be very different from what people think their ancestry is ... Is it possible that there is bias at work in the genetic study of the Jews, that researchers are predisposed to accept results that confirm what Jews believe about themselves, and to discount results at odds with that self-image? Possibly, but there have also been studies that suggest that in some contexts self-identity and genetically established ancestry can match up fairly well. That is what much of recent genetic research has been suggesting about the Jews: that there is a correspondence between what they believe about the origin of their ancestors and the genetic ancestry registered in their DNA, that they have an ancestry distinct from that of the non-Jews among whom they live, and that some of those ancestors came from the Near East.

There are considerably large amounts of common ancestry, but there is no single Jewish genotype; there is no single Jewish identity that can be established genetically in all cases. Continuities of vertical descent are observed, but gene flow both between Jewish communities, as well as with surrounding gentile communities was also intense. Kohler, commenting on three studies by Behar (2010), Atzmon (2010) and Ostrer (2012), concludes that they are not unique as "since from the 1950s onwards studies show that Jews from different geographic/ethnic backgrounds were somewhat related". Falk stated that, "(t)here are no 'Jewish genes,' even though there are plenty of mutations that are pretty much restricted to a certain group of Jews", a viewpoint endorsed by Robert Pollack, among others.

The questions posed by thinkers on race over a century ago have relevance to contemporary scholarly discussions and debates on the genetic origins of ethnic groups. Some earlier controversies persist, with similar juxtaposition of antithetical views, between scientific proponents and skeptics of Jewish genetic or racial distinctions. Schaffer illustrates the point by underscoring how the marked differences in the views of two English Jewish physician-scholars and colleagues, Charles Singer and Redcliffe Salaman, – the former indifferent to Zionism and the latter an ardent supporter of the movement – form two categories in an "intellectual schism" dividing Jewish thinkers on race, a schism that remains alive even after the lapse of a century. Schaffer concludes his overview of a half-century of strenuous studies, by declaring that an ideological intransigence in all parties to the dispute persists, and that "discussions of this nature are unlikely to come to synthesis any time soon and instead are destined to remain bogged down in religious dogma and political agendas".

According to Falk, "Even though not a race in a biological sense, political Zionism, after a century of attempts to prove contemporary Jews' material, biological relationships – not merely their spiritual, cultural ones – to the ancient people of the biblical stories, in spite of widespread interspersing with local communities, finally has succeeded. It is tragic that Zionism, as well as Arab Nationalism, have failed to recognize the Palestinians, many of whom similarly appear to share phylogenetic relations to the historic inhabitants of the country, as equal partners."

Since the 1990s, Israeli sociologist Uri Ram has identified the emergence of "Neo-Zionism, which, in contrast to classical, secular forms of Zionism, such as labour Zionism, he defines as "an exclusionary, nationalist, even racist, and antidemocratic political-cultural trend, striving to heighten the fence encasing Israeli identity".

Research into the medical genetics of Jews has identified factors associated with certain diseases known to affect Jews, though the share of genetic diseases among them is no greater than among any other population. Some 20 single gene mutations alone have been detected that affect the Ashkenazi, among them illnesses such as Tay–Sachs disease, Canavan disease, Gaucher's disease, Riley-Day syndrome, Niemann–Pick disease and Huntington's chorea and many other often fatal conditions, some associated particularly with, but not exclusively to, Jews. Institutions such as Dor Yeshorim have created a DNA database so that one can check for genetically incompatible matches among prospective couples.

According to Michael Satlow, Professor of Religious Studies and Judaic Studies at Brown University, whatever implications might be read into these researches, Jewish religious law and the Law of Return have not been affected by Jewish population genetics. Genetic research has raised issues that affect the definition of who a Jew is, and contemporary rabbinical discussions do address problems that arise from the impact of genetics and new reproductive technologies. While Rebecca Alpert cites the Tanakh for the idea that there is a theological basis for biology as part of being Jewish, the geneticist Robert Pollack has drawn on the authority of Maimonides to arrive at the opposite conclusion. In the Mishneh Torah, according to Pollack, the Rambam states that 'when hiring a teacher of Torah for yourself or your child, you should give a learned mamzer, (a child from an illicit union), precedence over an ignorant man, even if that ignorant man happens to be the Kohen Gadol himself.' The standard halakhic definition draws a distinction between a biological transmission of Jewishness (via the mother), and Jewishness as a matter of religious practice, extending to converts, and limiting the role of genes in Jewishness. Genetic evidence has been adduced to campaign for the right to aliyah for people like the Bantu Lemba, after indications turned up that their Buba priesthood were found to be bearers of the Y-chromosomal Aaron associated with the Cohanim who are, in Jewish tradition, thought to be direct descendants of the priestly caste that made sacrifices at the Second Temple.

The genetics of Jewish identity have given rise to concerns among historians specializing in Jewish studies who question the selective use of versions of traditional history in interpreting genetic data, and consider cross-disciplinary collaboration proposals confusing. The reliance of geneticists in framing their research in the area of Jewish genetics on traditional, indeed theological, stories about the Jewish past – a characteristic also of earlier race theories – is often construed as meaning that old religious narratives underpin the presuppositions informing the science itself. Some genetic works have claimed to have solved vexed conundrums in Jewish history like the origins of the Levites and Cohanim, while using core assumptions of Jewish tradition in their interpretations of the statistical data With such a trend, Schaffer argues, genetics is usurping Jewish history, a discipline which is properly the province of historians.

Genetic arguments linking modern Jews and those of ancient Israel lend themselves to Zionist national narratives, and have been described by Ostrer as the "biologization and consolidation" of Jewish national identity. Burton suggests that positioning modern Jews as the primary descendants of ancient Israelites underpins the legitimacy of the Zionist narrative, much as the controversial Phoenicianism did around the same time within Lebanese nationalism. The genetic affinity of Jews to Palestinians can be used to bolster claims that Jews originated in Israel. Anti-Zionists likewise have used genetics to support their critiques of Israel. Jarrod Tanny sums up the issue by remarking: "If nationalism is based on the premise of 'We were here first' and 'we Jews' were not here first, then the land is not 'ours,' and Zionism is little more than an instance of European colonialism." Falk noted that while Zionism has achieved its goal, it was in his view tragic that the very phenotypical evidence from genetics used to underpin its claims to the land suggests that many Palestinians also are related to Jews as equal partners .

A recent study by a team of international psychologists concluded that research into genetic differences could inflame political violence in the Israeli–Palestinian conflict, while highlighting genetic similarities could help reduce conflict. As McGonigle outlines, arguments over Ashkenazi descent fuel fierce controversies in the politics of Jewish genetics; critics of Israel may contest Zionism as a settler colonial project along genetic grounds.

• Jewish peoplehood
• Who is a Jew?
• Ethnic nationalism
• Genetic studies on Jews
• Race and genetics
• Racism in Israel
• Racism in Jewish communities
• Politics of archaeology in Israel and Palestine