We present a protocol for using paleomagnetic analysis to determine the absolute orientation of core recovered from the SAFOD borehole. Our approach is based on determining the direction of the primary remanent magnetization of a spot core recovered from the Great Valley Sequence during SAFOD Phase 2 and comparing its direction to the expected reference field direction for the Late Cretaceous in North America. Both thermal and alternating field demagnetization provide equally resolved magnetization, possibly residing in magnetite, that allow reorientation. Because compositionally similar siltstones and fine-grained sandstones were encountered in the San Andreas Fault Zone during Stage 2 rotary drilling, we expect that paleomagnetic reorientation will yield reliable core orientations for continuous core acquired from directly within and adjacent to the San Andreas Fault during SAFOD Phase 3, which will be key to interpretation of spatial properties of these rocks. Copyright 2008 by the American Geophysical Union.