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Congenital glaucoma is a well-recognized entity that can occur in the presence of anterior segment dysgenesis. Trabeculectomy is an accepted intervention in the management of congenital glaucoma. The surgical technique as well as complications is well described.This is a case report of a 3-month-old girl with anterior segment dysgenesis and glaucoma. She was referred post-trabeculectomy with persistent corneal opacity to be considered for penetrating keratoplasty and was found to have intrastromal corneal bleb.Ultrasound biomicroscopy confirmed communication of the corneal bleb with the anterior chamber, and the bleb was treated by autologous blood injection at the trabeculectomy site, under acetazolamide cover.We present evidence suggesting that abnormal structure was the etiologic basis for corneal bleb formation and describe our management of this previously unreported complication of trabeculectomy.