A phototherapeutic system for providing phototherapy to a patients lower parts of a gastrointestinal (GI) tract, the phototherapeutic system including a capsule sized and shaped for insertion into the rectum, the capsule including one or more phototherapeutic light sources. A method for intra-luminal phototherapy of the lower parts of the gastrointestinal (GI) tract including inserting a phototherapeutic device including one or more phototherapeutic light sources into the rectum, activating the light sources, and providing light at a dose suitable for providing a phototherapeutic effect. Related apparatus and methods are also described.