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Defects in closure of embryonic fissure and invagination of optic vesicle results in varied clinical presentation of microphthalmos with cyst. In our study, three patients had microphthalmos with cyst in one of their orbits. The cyst presented either as a swelling in the lower lid or as a sinus with purulent discharge associated with absent or small sized eyeball. The microphthalmic eye showed a spectrum of posterior segment abnormalities such as retinal disorganisation, gliosis, choroidal, and scleral coloboma. Microscopically, the cyst connected to the coloboma consisted of an outer layer of fibrovascular tissue and an inner gliotic neuroectodermal layer. The treatment consisted of excision of cyst alone or of microphthalmic eye with cyst. The use of conformers was mandatory after removal of cystic eyeball for near normal development of both orbits to maintain facial symmetry in our paediatric patients.