A case of autism with CHARGE syndrome with microphthalmos and a superior colobomatous cyst arising from the optic disc is reported. A 7-year-old boy presented with a gradually increasing mass, involving the superior orbit and upper eyelid of right eye of 3 years' duration. Clinical examination revealed bilateral microphthalmos with typical iris coloboma, posterior synechiae, and cataractous lens. Imaging revealed bilateral optic disc colobomas with a superior cyst in the right orbit. Intraoperatively, a single cystic lesion was seen in the superior orbit arising from the optic disc region. Histopathology was suggestive of a colobomatous cyst, positive for glial tissue [glial fibrillary acidic protein (GFAP) positive] and neuroretinal elements (synaptophysin positive) on immunohistochemistry. Genetic analysis revealed a normal karyotype (46, XY).