The San Andreas Fault Observatory at Depth (SAFOD) was drilled to study the physical and chemical processes controlling faulting and earthquake generation along an active, plate-bounding fault at depth. SAFOD is located near Parkfield, California and penetrates a section of the fault that is moving due to a combination of repeating microearthquakes and fault creep. Geophysical logs define the San Andreas Fault Zone to be relatively broad (~200 m), containing several discrete zones only 2–3 m wide that exhibit very low P- and S-wave velocities and low resistivity. Two of these zones have progressively deformed the cemented casing at measured depths of 3192 m and 3302 m. Cores from both deforming zones contain a pervasively sheared, cohesionless, foliated fault gouge that coincides with casing deformation and explains the observed extremely low seismic velocities and resistivity. These cores are being now extensively tested in laboratories around the world, and their composition, deformation mechanisms, physical properties, and rheological behavior are studied. Downhole measurements show that within 200 m (maximum) of the active fault trace, the direction of maximum horizontal stress remains at a high angle to the San Andreas Fault, consistent with other measurements. The results from the SAFOD Main Hole, together with the stress state determined in the Pilot Hole, are consistent with a strong crust/weak fault model of the San Andreas. Seismic instrumentation has been deployed to study physics of faulting—earthquake nucleation, propagation, and arrest—in order to test how laboratory-derived concepts scale up to earthquakes occurring in nature.