There is an increasing need for real-time implementation of 3D image analysis processes, especially in the context of image-guided surgery. Among the various image analysis tasks, non-rigid image registration is particularly needed and is also computationally prohibitive. This paper presents a GPU (Graphical Processing Unit) implementation of the popular Demons algorithm using a Gaussian recursive filtering. Acceleration of the classical method is mainly achieved by a new filtering scheme on GPU which could be reused in or extended to other applications and denotes a significant contribution to the GPU-based image processing domain. This implementation was able to perform a non-rigid registration of 3D MR volumes in less than one minute, which corresponds to an acceleration factor of 10 compared to the corresponding CPU implementation. This demonstrated the usefulness of such method in an intra-operative context.