We demonstrate a technique for estimating the location of the hippocampus in MRI and CT images for use in radiotherapy treatment planning, using both rigid and contour based deformable image registration. The automatically generated contours can be subsequently modified for a given patient. By mapping the hippocampi from several patients into a template image set, a population-based average hippocampal atlas was generated. Approximate hippocampal contours can be automatically generated in a given image set by mapping this atlas onto it. The performance and accuracy of several atlases generated in different ways was tested on 10 MRI images and 7 CT images. Auto-contouring based on deformable registration significantly outperformed that based on rigid registration alone, with an average Dice similarity score of 0.62 (range .40-.76) for methods utilizing deformation. Comparable results were achieved in auto-contouring CT images when deformable registration was used, demonstrating that the methodology is robust with respect to imaging modality.