To ensure accurate targeting and repeatability, 3D TRUS-guided biopsies require registration to determine coordinate transformations to (1) incorporate pre-procedure biopsy plans and (2) compensate for inter-session prostate motion and deformation between repeat biopsy sessions. We evaluated prostate surface- and image-based 3D-to-3D TRUS registration by measuring the TRE of manually marked, corresponding, intrinsic fiducials in the whole gland and peripheral zone, and also evaluated the error anisotropy. The image-based rigid and non-rigid methods yielded the best results with mean TREs of 2.26 mm and 1.96 mm, respectively. These results compare favorably with a clinical need for an error of less than 2.5 mm.