We examine the relationships between borehole geophysical data and physical properties of fault-related rocks within the San Andreas Fault as determined from data from the San Andreas Fault Observatory at Depth borehole. Geophysical logs, cuttings data, and drilling data from the region 3- to 4-km measured depth of the borehole encompass the active part of the San Andreas Fault. The fault zone lies in a sequence of deformed sandstones, siltstone, shale, serpentinite-bearing block-in-matrix rocks, and sheared phyllitic siltstone. The borehole geophysical logs reveal the presence of a low-velocity zone from 3190 to 3410 m measured depth with V-p and V-s values 10-30% lower than the surrounding rocks and a 1-2 m thick zone of active shearing at 3301-3303 m measured depth. Seven low-velocity excursions with increased porosity, decreased density, and mud-gas kick signatures are present in the fault zone. Geologic data on grain-scale deformation and alteration are compared to borehole data and reveal weak correlations and inverse relationships to the geophysical data. In places, V-p and V-s increase with grain-scale deformation and alteration and decrease with porosity in the fault zone. The low-velocity zone is associated with a significant lithologic and structural transition to low-velocity rocks, dominated by phyllosilicates and penetratively foliated, sheared rocks. The zone of active shearing and the regions of low sonic velocity appear to be associated with clay-rich rocks that exhibit fine-scale foliation and higher porosities that may be a consequence of the fault-related shearing of foliated and fine-grained sedimentary rocks.