Recovered core samples from the San Andreas Fault Observatory at Depth (SAFOD), located near Parkfield, CA, offer a unique opportunity to study the products of faulting and to learn about the mechanisms of slip at 3 km depth. Casing deformation reflects active creep along two strands of the San Andreas Fault (SAF) at SAFOD. The two fault strands are referred to as the Southwest Deforming Zone (SDZ) at 3194 m measured depth (MD) and the Central Deforming Zone (CDZ) at 3301 m MD. The SDZ and CDZ contain remarkably similar gouge layers, both of which consist of a clay-bearing, ultrafine grain matrix containing survivor clasts of sandstone and serpentinite. The two gouges have sharp boundary contacts with the adjacent rocks. We have used X-ray Computed Tomography (XCT) imaging, at two different sampling resolutions, to investigate the mesoscale and microscale structure of the fault zone, specifically to characterize the shape, preferred orientation, and size distribution of the survivor clasts. Using various image processing techniques, survivor clast shape and size are characterized in 3D by best-fit ellipsoids. Renderings of survivor clasts illustrate that survivor clasts have fine tips reminiscent of sigma type tails of porphyroclasts observed in myolonites. The resolution of the XCT imaging permits characterization of survivor clasts with equivalent spherical diameters greater than 0.63 mm. The survivor clast population in both the SDZ and CDZ gouge layers have similar particle size distributions (PSD) which fit a power law with a slope of approximately -3; aspect ratio (major to minor axis ratios) distributions also are similar throughout ranging between 1.5 and 4, with the majority occurring between 2-2.5. The volume- and shape- distributions vary little with position across the gouge zones. A strong shape preferred orientation (SPO) exists in both creeping zones. In both the SDZ and CDZ the minor axes form a SPO approximately normal to the plane of the San Andreas Fault (SAF), and the major axes define a lineation in the plane of the SAF. The observation that the size-, shape- and orientation-distributions of mesoscale, matrix-supported clasts are similar in the SDZ and CDZ gouge layers, and vary little with position in each gouge layer, is consistent with the hypothesis that aseismic creep in the SDZ and CDZ is achieved by distributed, shearing. The consistency between the SPO and simple-shear, strike-slip kinematics, and the marked difference of PSD, fabric, cohesion and clast lithology of the gouge with that of the adjacent rock, is consistent with the hypothesis that the vast majority of the shear displacement on the SAF at SAFOD is accommodated within the gouge layers and the gouge displays a mature, nearly steady-state structure.