We report a case of cystic lesion in a 37-year-old woman. The patient had an oval-shaped lesion adjacent to the temporomandibular joint. Thick fibrotic tissue and muscle were observed microscopically, but the epithelium lining was not observed. The lesion was diagnosed as a ganglion cyst. The patient's general medical history was non-contributory. High performance liquid chromatography (HPLC) and mass spectrophotometry (MS) revealed some proteins from the fluid in the lesion, such as a filaggrin precursor, dystroglycan, a polyprotein of the hepatitis C virus, and proteins originating from bacteria. The follow-up examinations revealed no recurrence. The probable pathogenesis of the lesion is discussed.