The introduction of prior knowledge has greatly enhanced numerous purely low-level driven image processing algorithms. In this work, we focus on the problem of nonrigid image registration. A number of powerful registration criteria have been developed in the last decade, most prominently the criterion of maximum mutual information. Although this criterion provides for good registration results in many applications, it remains a purely low-level criterion. As a consequence, registration results will deteriorate once this low-level information is corrupted, due to noise, partial occlusions or missing image structure. In this paper, we will develop a Bayesian framework that allows to impose statistically learned prior knowledge about the joint intensity distribution into image registration methods. The prior is given by a kernel density estimate on the space of joint intensity distributions computed from a representative set of pre-registered image pairs. This nonparametric prior accurately models previously learned intensity relations between various image modalities and slice locations. Experimental results demonstrate that the resulting registration process is more robust to missing low-level information as it favors intensity correspondences statistically consistent with the learned intensity distributions.