We present a method with fusion of images of three modalities 18F-FDG PET, CT, and 3-D ultrasound (US) applied to imaging of the anal canal and the rectum. To obtain comparable geometries in the three imaging modalities, a plexiglas rod, with the same dimensions as the US transducer, is placed in the anal canal prior to the PET-CT examination. The method is based on manual co-registration of PET-CT images and 3-D US images. The three-modality imaging of the rectum-anal canal may become useful as a supplement to conventional imaging in the external radiation therapy in the treatment of anal cancer, where the precise delineation of a tumor is crucial to avoid damage from radiation therapy to the healthy tissue surrounding it. The technique is still in a phase of development, and the demands for integration different company software systems are significant before commercial application. Three-modality imaging may also be used in certain other diagnostic or therapeutic fields.