We present a new fast implementation of a non-rigid registration algorithm, based on a finite element elastic deformation model using the mutual information metric with a linear elastic regularization constraint. The algorithm was parallelized for symmetric multi-processor architectures. A Simultaneous Perturbation Stochastic Approximation (SPSA) optimization scheme was used to maximize the objective function. This algorithm was applied to capture non-rigid deformations of pre-procedural to post-procedural images of tumor Radio-Frequency (RF) ablation in the liver and nonrigid deformationsof intra-operative to pre-operativeprostate images.