Synovial chondromatosis (SC) involving the temporomandibular joint (TMJ) is very rare and can occur in either or both cavities. Differentiation of the affected cavity in SC is therefore as important as making the diagnosis. This report presents a case of SC in which both cavities were thought to be affected, but arthrography using cone beam CT (CBCT) allowed us to see that involvement was limited to the superior joint cavity. In addition, we describe the usefulness of arthrographic CBCT for diagnosis and treatment planning in SC of the TMJ.