Abstract Atypical rift features have been described using 2D and 3D SPOT imagery over the dominantly Pleistocene lavas and sedimentary deposits that cover the axial graben of the Kenya Rift. These structures are interpreted to be the result of isolated oblique basement heterogeneities within a more or less heterogeneous substratum formed by Neogene lava flows which overlie crystalline Precambrian basement. The observed atypical fault geometries within the axial graben of Baringo-Bogoria and Magadi areas are thought to be influenced by: the magnitude of heterogeneity in the substratum; the angle of such heterogeneities with respect to the main trend of the rift; and the scale of the distribution of these heterogeneities. The authors propose that oblique substratum heterogeneities reflect the location of strands of mylonitic shear zones related to the major Proterozoic Aswa structure within the Precambrian basement. Extensional deformation applied on such basement forms generates, in the cover, a series of atypical fault systems of different magnitude, angle, and distribution from the general fault patterns in the Kenya Rift.