This paper proposes a general method for establishing pairwise correspondences, which is a fundamental problem in image analysis. The method consists of over-segmenting a pair of images into supervoxels. A forest classifier is then trained on one of the images, the source, by using supervoxel indices as voxelwise class labels. Applying the forest on the other image, the target, yields a supervoxel labelling which is then regularized using majority voting within the boundaries of the target’s supervoxels. This yields semi-dense correspondences in a fully automatic, efficient and robust manner. The advantage of our approach is that no prior information or manual annotations are required, making it suitable as a general initialisation component for various medical imaging tasks that require coarse correspondences, such as, atlas/patch-based segmentation, registration, and atlas construction. Our approach is evaluated on a set of 150 abdominal CT images. In this dataset we use manual organ segmentations for quantitative evaluation. In particular, the quality of the correspondences is determined in a label propagation setting. Comparison to other state-of-the-art methods demonstrate the potential of supervoxel classification forests for estimating image correspondences.