The San Andreas fault accommodates 28–34 mm yr⁻¹ of right lateral motion of the Pacific crustal plate northwestward past the North American plate. In California, the fault is composed of two distinct locked segments that have produced great earthquakes in historical times, separated by a 150-km-long creeping zone. The San Andreas Fault Observatory at Depth (SAFOD) is a scientific borehole located northwest of Parkfield, California, near the southern end of the creeping zone. Core was recovered from across the actively deforming San Andreas fault at a vertical depth of 2.7 km (ref. 1). Here we report laboratory strength measurements of these fault core materials at in situ conditions, demonstrating that at this locality and this depth the San Andreas fault is profoundly weak (coefficient of friction, 0.15) owing to the presence of the smectite clay mineral saponite, which is one of the weakest phyllosilicates known. This Mg-rich clay is the low-temperature product of metasomatic reactions between the quartzofeldspathic wall rocks and serpentinite blocks in the fault^2,3. These findings provide strong evidence that deformation of the mechanically unusual creeping portions of the San Andreas fault system is controlled by the presence of weak minerals rather than by high fluid pressure or other proposed mechanisms¹. The combination of these measurements of fault core strength with borehole observations^1,4,5 yields a self-consistent picture of the stress state of the San Andreas fault at the SAFOD site, in which the fault is intrinsically weak in an otherwise strong crust.