This book constitutes the thoroughly refereed post-proceedings of the Third International Workshop on Biomedical Image Registration, WBIR 2006, held in Utrecht, The Netherlands, in July 2006. The 20 revised full papers and 18 revised poster papers presented were carefully reviewed and selected for inclusion in the book. The papers cover all areas of biomedical image registration; methods of registration, biomedical applications, and validation of registration. Topics addressed are measures of similarity, 2D/3D/4D, nonrigid deformation, intra- or inter-modality registration, intra- or inter-subject registration, optimization methods, model-based registration, computer integrated surgery, image-guided therapy and diagnosis, treatment planning, serial studies, morphometry, biomechanics, image retrieval, image tiling and image fusion, computational and empirical accuracy, comparison studies, and physical models.