We managed three cases of congenital iris stromal cysts and compared them with 22 cases in the published reports to delineate the clinical features of this condition and determine the best treatment. Our first patient, a 5-month-old girl, had injection of a cyst with trichloroacetic acid, but developed a cataract and endothelial damage to the cornea and the eye was eventually enucleated. Our second patient, a 9-week-old girl, was treated with repeated xenon photocoagulation, drainage of the cyst, and cryotherapy, but required enucleation of the eye. Our third patient, a 5-month-old girl, had excision of the cyst by sector iridectomy with preservation of vision and no recurrence two years later. Our results suggest that complete surgical excision is a superior method of treatment for congenital cysts of the iris stroma.