A method and system for dual energy image registration is disclosed. In order to segment first and second images of a dual energy image pair, the first and second images are preprocessed to detect edges in the images. Gaussian pyramids, having multiple pyramid images corresponding to multiple pyramid levels, are generated for the first and second images. An initial optical flow value is initialized for a first pyramid level, and the optical flow value is sequentially updated for each pyramid level based on the corresponding pyramid images using an optimization function having a similarity measure and a regularizer. This results in a final optical flow value between the first and second images, and the first and second images are registered based on the final optical flow value.