Three patients had microphthalmos with cyst in one orbit and contralateral congenital cystic eye, microphthalmos alone, or microphthalmos with cyst. Four eyes were examined histopathologically. The microphthalmic eye demonstrated a spectrum of anterior segment abnormalities, retinal disorganization and gliosis, and a choroidal and scleral colomboma. The cyst connected to the colobona consisted of an outer fibrovascular layer and inner gliotic neuroectodermal layer. The cyst probably originated from proliferation of neuroectodermal tissue at the edge of a persistently open embryonic fissure. Treatment consisted of multiple aspirations of the cyst, excision of the cyst alone, and excision of both the microphthalmic eye and cyst.