In this paper we present 3D registration techniques for detecting breast cancer lesions based on differences between the high spatial resolution 'pre' and 'post' contrast administration MR breast scans. We also present registration techniques for detecting lesions based on the time course of enhancement after administration of the contrast agent based on changes in the low spatial resolution, high temporal resolution, dynamic MR data taken during the absorption of the contrast agent. Alignment of the 'pre' and 'post' MR data and of the dynamic MR images is done by a direct optimization technique to estimate a global affine deformation model using a coarse-to-fine control strategy over a 3D pyramid. This global model is followed by a one iteration flow estimation to account for any local non-rigidity. We present results of the registration process and visualization of the difference volumes obtained after alignment.