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The drilling of a deep borehole across the actively creeping Parkfield segment of the San Andreas Fault Zone (SAFZ), California, and collection of core materials permit direct geological study of fault zone processes at 2–3 km depth. The three drill cores sample both host and fault rocks and pass through two currently active, narrow (1–2 m wide) shear zones enclosed within a broader (ca. 240 m wide) region of inactive foliated gouges. The host rocks preserve primary sedimentary features and are cut by numerous minor faults and small, mainly calcite-filled veins. The development of Fe-enriched smectitic phyllosilicate networks following cataclasis is prevalent in the presently inactive foliated gouges of the main fault zone and in minor faults cutting clay-rich host rocks. Calcite, anhydrite and minor smectitic phyllosilicate veins are interpreted to have formed due to local fluid overpressuring events prior to, synchronous with and after local gouge development. By contrast, the active shear zone gouges lack mineral veins (except as clasts) and contain numerous clasts of serpentinite. Markedly Mg-rich smectitic phyllosilicates are the dominant mineral phases here, suggesting that the fault zone fluids have interacted with the entrained serpentinites. We propose that weakening of the SAFZ down to depths of at least 3 km can be attributed to the pervasive development of interconnected networks of low friction smectitic phyllosilicates and to the operation of stress-induced solution-precipitation creep mechanisms.