This book constitutes the thoroughly refereed post-proceedings of the Second International Workshop on Biomedical Image Registration, WBIR 2003, held in Philadelphia, PA, USA in June 2003.The 20 revised full papers and 20 revised poster papers presented together with an invited paper and the abstract of an invited paper were carefully reviewed and improved during two rounds of reviewing and revision. The papers are organized in topical sections on regularization, novel approaches, brain image registration, piecewise affine registration, information theoretic issues, interventional imaging, and applications.