Intraoral phototherapy devices receive light from an associated light source and propagate the light into an oral cavity of a patient. The device comprises a light guide that receives light from an external light source. The light guide comprises a main body portion made of an optically transparent soft flexible biocompatible polymeric material sized and shaped to conform to contours of the oral cavity when inserted therein to direct the light to targeted regions of the oral cavity. The main body portion comprises a pair of spaced apart side wings sized and shaped to be received between a patient's teeth and cheeks on opposite sides of the oral cavity and a center flap intermediate the side wings for transmitting and directing the light to targeted regions of the oral cavity. A controller delivers light to the light guide in a controlled manner.