File:Iconography - Saint Basil's Cathedral (19970306871).jpg
Instead of following the original ad hoc layout (seven churches around the central core), Ivan's architects opted for a more symmetrical floor plan with eight side churches around the core, producing "a thoroughly coherent, logical plan" despite the erroneous latter "notion of a structure devoid of restraint or reason" influenced by the memory of Ivan's irrational atrocities. The central core and the four larger churches placed on the four major compass points are octagonal; the four diagonally placed smaller churches are cuboid, although their shape is barely visible through later additions. The larger churches stand on massive foundations, while the smaller ones were each placed on a raised platform, as if hovering above ground. Although the side churches are arranged in perfect symmetry, the cathedral as a whole is not. The larger central church was deliberately offset to the west from the geometric center of the side churches, to accommodate its larger apse on the eastern side. As a result of this subtle calculated asymmetry, viewing from the north and the south presents a complex multi-axial shape, while the western facade, facing the Kremlin, appears properly symmetrical and monolithic. The latter perception is reinforced by the fortress-style machicolation and corbeled cornice of the western Church of Entry into Jerusalem, mirroring the real fortifications of the Kremlin. Inside the composite church is a labyrinth of narrow vaulted corridors and vertical cylinders of the churches. The largest, central one, the Church of the Intercession, is 46 meters tall internally but has a floor area of only 64 square meters. Nevertheless, it is wider and airier than the church in Kolomenskoye with its exceptionally thick walls. The corridors functioned as internal parvises; the western corridor, adorned with a unique flat caissoned ceiling, doubled as the narthex.
The detached belfry of the original Trinity Church stood southwest or south from the main structure. Late 16th and early 17th century plans depict a simple structure with three roof tents, most likely covered with sheet metal. No buildings of this type survived to date, although it was then common and used in all of the pass-through towers of Skorodom. August von Meyerberg's panorama (1661) presents a different building, with a cluster of small onion domes.