Conjunctival swabs were used in combination with polymerase chain reactions (PCR) or virus culture to aid to confirm the diagnosis of cytomegalovirus (CMV) retinitis in AIDS patients. Based on ophthalmoscopic findings, 13 AIDS patients were diagnosed as having CMV retinitis and treated with systemic ganciclovir from January 1997 to December 1998. Nine of 13 AIDS patients with CMV retinitis were found to be positive for CMV DNA by using a conjunctival swab with PCR (CS-PCR). CMV was also isolated from the conjunctival swab culture in 2 AIDS patients with CMV retinitis. Following 1 month of systemic ganciclovir treatment, except for 1 patient who had disease progression and remained positive for CMV DNA by using CS-PCR, 12 patients were negative for CMV with a concordant lesion regression. Results of this study also indicate that this CS-PCR method is valuable for confirming the diagnosis of CMV retinitis and monitoring the ganciclovir effect on the treatment of CMV retinitis in AIDS patients.