In this paper we present coupled partial differential equations (PDEs) for the problem of joint segmentation and registration. The registration component of the method estimates a deformation field between boundaries of two structures. The desired coupling comes from two PDEs that estimate a common surface through segmentation and its non-rigid registration with a target image. The solutions of these two PDEs both decrease the total energy of the surface, and therefore aid each other in finding a locally optimal solution. Our technique differs from recently popular joint segmentation and registration algorithms, all of which assume a rigid transformation among shapes. We present both the theory and results that demonstrate the effectiveness of the approach.