Hydrologic rock properties are important to the debate about the state of stress and heat flow regime of the San Andreas fault. In particular, these properties are pertinent to whether frictional heat generated by high shear stresses can be convected away by circulating ground water, thus accounting for the absence of a measurable heat flow anomaly across the fault. To help resolve this debate, we have conducted laboratory permeability measurements on intact core samples from the Cajon Pass drill hole extracted from depths between 2100 and 3500 m. These rocks were all crystalline in nature, including granodiorites, tonalites, monzogranites and gneisses. Confining and pore pressures matched the in situ pressures for each depth, and distilled water was used as the permeating medium. Permeabilities ranged from 10⁻²² to 10⁻¹⁹ m² for effective pressures between 36 and 56 MPa. In general, the permeability values decreased with depth in a manner consistent with earlier studies of rocks between 500 and 2100 m in the drill hole. Petrographic observations indicate that repeated episodes of crack healing and sealing are the mechanisms responsible for the extremely low permeability values. Secondary minerals that seal the microfractures include abundant laumontite, calcite, quartz, chlorite, and other phyllosilicates. The permeability results suggest that water circulation in the vicinity of the drill hole must be restricted to major fracture zones, with minimal exchange of water in more intact regions. This finding is consistent with geochemical evidence of little mixing of the pore waters sampled from different sections of the borehole. The results also suggest that massive water circulation through the bulk of the rock is unlikely as a mechanism for obscuring the heat flow anomaly that would be expected if shear stresses along the San Andreas fault are high.