A comprehensive suite of geophysical logs was collected in the SAFOD Pilot Hole from a depth of 775 m to 2150 m in highly fractured Salinian granite. The Pilot Hole intersected numerous macroscopic fractures and faults with extremely varied orientations. Despite the highly variable orientation of the fractures and faults, the fast polarization direction of the shear waves is very consistent with the direction of maximum horizontal compression determined from wellbore breakouts and drilling induced tensile fractures. At least three major shear zones were intersected by the borehole that are characterized by anomalously low velocity and resistivity, anomalously high shear velocity anisotropy and an absence of stress-induced wellbore breakouts (which suggests anomalously low differential stress). We argue that the physical mechanism responsible for the seismic velocity anisotropy observed in the Pilot Hole is the preferential closure of fractures in response to an anisotropic stress state.