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This paper focuses mainly on development of an efficient affine registration scheme for multimodality images. The stochastic gradient optimization of mutual information is accomplished using a simultaneous perturbation stochastic approximation (SPSA) technique to do the tuning of the affine parameters. The experimental results show that the SPSA based stochastic gradient optimization is strong for the multimodality image registration. The main contribution of this paper is that we extended the SPSA technique to simultaneously register the affine transformation for more than two images, and successfully accomplished the SPSA based stochastic gradient algorithm to optimize the information theory based similarity measure such as mutual information.