In order to reduce registration time, improve convergence ability and perform better in the presence of noise, a novel medical image registration measure is proposed, which is called generalized Jensen-Schur measure. According to Jensen-Schur measure, two kinds of special measures are constructed: Jensen-Schur- alpha and Jensen-Rényi-alpha. The characters of the two measures, mutual information and normalized mutual information are analyzed and compared by applying them to rigid registration of magnetic resonance (MR)/computed tomography (CT) and MR/positron emission tomography (PET) images. The results of tests show that Jensen-Schur-alpha (alpha = 2 or 3) outperforms other measures in the computational speed, convergence performance and noise immunity.