Forty patients were diagnosed as having complex microphthalmos on the basis of a malformed globe with a total axial length measurement at least 2 SDs below the mean for age-similar controls. Three had anterior segment dysgenesis; 4, congenital lens abnormalities; 14, chorioretinal colobomas; 12, persistent hyperplastic primary vitreous; 4, retinal dysplasia; and 3, complex malformations due to ipsilateral facial malformations. Measurements of total axial length indicated that complex microphthalmos was congenital and that postnatal growth of the malformed eye was similar to that of normal eyes. In most patients the anterior segment length was normal, while in all patients the posterior segment length was at least 2 SDs below the mean. Corneal diameter correlated significantly with total axial length (r2 = .57) and decreased linearly as total axial length decreased. In most patients in whom measurements were obtained, the lens and corneal power were increased, thereby compensating for decreased total axial length. We propose that inadequate production of secondary vitreous is the cause of the microphthalmos, given that the posterior segment was disproportionately reduced in size and the secondary vitreous is its predominant component. Evidence that each of the various ocular malformations can influence the production of secondary vitreous is presented.