Purpose: We present a fully automatic algorithm for the segmentation of the prostate in three-dimensional magnetic resonance (MR) images. Method: Our approach requires the use of an anatomical atlas which is built by computing transformation fields mapping a set of manually segmented images to a common reference. These transformation fields are then applied to the manually segmented structures of the training set in order to get a probabilistic map on the atlas. The segmentation is then realized through a two stage procedure. In the first stage, the processed image is registered to the probabilistic atlas. Subsequently, a \textit{probabilistic segmentation} is obtained by mapping the probabilistic map of the atlas to the patient's anatomy. In the second stage, a deformable surface evolves towards the prostate boundaries by merging information coming from the \textit{probabilistic segmentation}, an \textit{image feature model} and a \textit{statistical shape model}. During the evolution of the surface, the \textit{probabilistic segmentation} allows the introduction of a \textit{spatial constraint} that prevents the deformable surface from leaking in an unlikely configuration. Results: The proposed method is evaluated on 36 exams, that were manually segmented by a single expert. A median Dice similarity coefficient of 0.86 and an average surface error of 2.41 mm are achieved. Conclusion: By merging prior knowledge, the presented method achieves a robust and completely automatic segmentation of the prostate in MR images. Results show that the use of a \textit{spatial constraint} is useful to increase the robustness of the deformable model comparatively to a deformable surface that is only driven by an image appearance model.