We have developed a nonrigid registration technique applicable to breast tissue imaging. It relies on a finite element method (FEM) model and a set of fiducial skin markers (FSMs) placed on the breast surface. It can be applied for both intra- and intermodal breast image registration. The registration consists of two steps. First, location and displacements of corresponding FSM observed in both moving and target volumes are determined, and then FEM is used to distribute the FSM displacements linearly over the entire breast volume. After determining the displacements at all the mesh nodes, the moving breast volume is registered to the target breast volume using an image-warping algorithm. In the second step, to correct for any residual misregistration, displacements are estimated for a large number of corresponding surface points on the moving and the target breast images, already aligned in 3D, and our FEM model and the warping algorithm are applied again. Our non-rigid multimodality and intramodality breast image registration method yielded good quality images with target registration error comparable with pertinent imaging system spatial resolution.