A non-parametric (NP) sampling method is introduced for obtaining the joint distribution of a pair of images. This method based on NP windowing and is equivalent to sampling the images at infinite resolution. Unlike existing methods, arbitrary selection of kernels is not required and the spatial structure of images is used. NP windowing is applied to a registration application where the mutual information (MI) between a reference image and a warped template is maximised with respect to the warp parameters. In comparisons against the current state of the art MI registration methods NP windowing yielded excellent results with lower bias and improved convergence rates.