A 13-day-old girl was referred for evaluation of a right orbital mass. Ophthalmic examinations revealed microphthalmia with cyst in the right eye and microphthalmia in the left eye. She had lowset ears, auricular fistula, micrognathia, and muscular hypotonia. Chromosomal analysis using fluorescence in-situ hybridization (FISH) showed partial trisomy 22. To our knowledge, microphthalmos with cyst associated with partial trisomy 22 has not been described previously in the English literature. Repeated aspiration resulted in a decrease in size of the cyst.