We examine drill cuttings from the San Andreas Fault Observatory at Depth (SAFOD) boreholes to determine the lithology and deformational textures in the fault zones and host rocks. Cutting samples represent the lithologies from 1.7-km map distance and 3.2-km vertical depth adjacent to the San Andreas Fault. We analyzed two hundred and sixty-six grain-mount thin-sections at an average of 30-m-cuttings sample spacing from the vertical 2.2-km-deep Pilot Hole and the 3.99-km-long Main Hole. We identify Quaternary and Tertiary(?) sedimentary rocks in the upper 700 m of the holes; granitic rocks from 760–1920 m measured depth; arkosic and lithic arenites, interbed-ded with siltstone sequences, from 1920 to ∼3150 m measured depth; and interbed-ded siltstones, mudstones, and shales from 3150 m to 3987 m measured depth. We also infer the presence of at least five fault zones, which include regions of damage zone and fault core on the basis of percent of cataclasite abundances, presence of deformed grains, and presence of alteration phases at 1050, 1600–2000, 2200–2500, 2700–3000, 3050–3350, and 3500 m measured depth in the Main Hole. These zones are correlated with borehole geophysical signatures that are consistent with the presence of faults. If the deeper zones of cataclasite and alteration intensity connect to the surface trace of the San Andreas Fault, then this fault zone dips 80–85° southwest, and consists of multiple slip surfaces in a damage zone ∼250–300 m thick. This interpretation is supported by borehole geophysical studies, which show this area is a region of low seismic velocities, reduced resistivity, and variable porosity.