To determine the mode of inheritance of congenital glaucoma, segregation analysis was performed using two different models: the transmission probability model and the mixed model. Whereas the latter, testing for monogenic inheritance in the presence of both monogenic and polygenic components, results in strong evidence for a major locus, the former, testing for Mendelian segregation at one locus, rejects this hypothesis. The differences in the results of these two models are discussed and are attributed to the underlying structure of each. Genetic heterogeneity of congenital glucoma is proposed.