Molecular biology is a young scientific discipline that has already had a profound impact on biomedical science, including basic and clinical eye research. In the coming years, molecular advances will increasingly influence aspects of diagnosis, prognosis, and therapy in clinical ophthalmology. Our current understanding of ocular pathophysiology and classification of eye disease will be advanced and challenged by new discoveries in molecular biology. A knowledge of genotype can clarify apparent phenotype. At the present time, diagnostic tests in ophthalmology for both acquired and inherited diseases are being revolutionized by molecular technology. The molecular genetics of ocular disease is currently the subject of intense investigation using techniques of gene mapping and isolation. Rapid progress in understanding the molecular basis of eye diseases will advance the treatment of these conditions, including the potential for gene therapy.