Abstract In this paper we present a novel method for computing the Mutual Information of images using recently developed non-equidistant fast Fourier-transform (NFFT) techniques. Standard approaches suffer from the problem that some sort of quantization is needed in order to apply a fast equidistant FFT-technique. For the new method no quantization is necessary which on one hand leads to an improved registration accuracy and on the other hand to a straight forward implementation. The evaluation is done for MR brain registration as well as for synthetic examples.