The registration problem for images of a deforming surface has been well studied. External occlusions are usually well-handled. In 2D image-based registration, selfocclusions are more challenging. Consequently, the surface is usually assumed to be only slightly self-occluding.This paper is about image-based non-rigid registration with self-occlusion reasoning. A specific framework explicitly modeling self-occlusions is proposed. It is combined with an intensity-based, i.e. direct, data term for registration. Self-occlusions are detected as shrinking areas in the 2D warp.Experimental results on several challenging datasets show that our approach successfully registers images with self-occlusions while effectively detecting the occluded regions.