A ganglion is a fluid-filled cyst with a myxoid matrix that occasionally occurs within muscles, tendons, and menisci. Ganglion cysts within the knee joint are rare. We report a case of multiple ganglion cysts in the intra-articular and extra-articular knee joint of a 36-year-old man. The diagnosis of ganglion within the knee joint was established by magnetic resonance imaging and confirmed by pathological examination. The patient underwent combined arthroscopy and open excision, and was free of symptoms at 36-month follow-up. Conservative treatment is recommended until the size or location of the cyst impairs function or causes significant disturbances in movement