Oral phototherapy applicators are disclosed that sized and shaped so as to fit at least partially in a user's mouth and adapted to conform to the shape of at least a portion of the oral cavity and have at least one radiation emitter coupled to an applicator body to irradiate a portion of the oral cavity with phototherapeutic radiation. The apparatus is configured to direct radiation to at least one portion of the oral cavity, e.g. a tooth, cheek, tongue, palate, throat and facial tissue, lymphatic tissue, blood, gland, follicle, collagen and pigmentation. In one embodiment, the apparatus body is compliant to facilitate conformation to a portion of the oral cavity.