The source of infecting bacteria is often unknown in postoperative endophthalmitis. Using techniques of molecular epidemiology, the authors demonstrate that an organism isolated from the vitreous was genetically indistinguishable from an isolate recovered from the patient's eyelid, conjunctiva, or nose in 14 (82%) of 17 cases of endophthalmitis. In two cases of Staphylococcus epidermidis endophthalmitis, after cataract surgery was performed by the same surgeon on the same day, genetic analysis demonstrated that the infecting organisms from the two patients' vitreous were distinct, and, furthermore, that in each case the external isolates were indistinguishable from the vitreous isolate. The results implicate the patients' external tissues as the source of the infecting organism in those cases of acute postoperative endophthalmitis studied. Therefore, attention should be directed toward the external tissues and their microbial flora in the prophylaxis and prevention of postoperative bacterial endophthalmitis.