In this paper, we present a new multimodal image registration method based on the a priori knowledge of the class label mappings between two segmented input images. A joint class histogram between the image pairs is estimated by assigning each bin value equal to the total number of occurrences of the corresponding class label pairs. The discrepancy between the observed and expected joint class histograms should be minimized when the transformation is optimal. Kullback-Leibler distance (KLD) is used to measure the difference between these two histograms. Based on the probing experimental results on a synthetic dataset as well as a pair of precisely registered 3D clinical volumes, we showed that, with the knowledge of the expected joint class histogram, our method obtained longer capture range and fewer local optimal points as compared with the conventional Mutual Information (MI) based registration method. We also applied the proposed method to 2D-3D rigid registration problems between DSA and MRA volumes. Based on manually selected markers, we found that the accuracies of our method and the MI-based method are comparable. Moreover, our method is more computationally efficient than the MI-based method.