To investigate the role of antiviral drug resistance in cytomegalovirus (CMV) disease progression, CMV cultured from an AIDS patient who developed progressive CMV disease despite continual anti- CMV treatment was characterized. In 7 CMV isolates, 1 ganciclovir-resistant strain predominated. Ganciclovir-resistant CMV, containing a UL97 mutation, was cultured from blood and urine before clinical indication of CMV central nervous system (CNS) disease, suggesting that the development of ganciclovir resistance preceded the dissemination of CMV to the CNS. Quantitative competitive polymerase chain reaction indicated that the isolation of ganciclovir-resistant CMV was concurrent with increased CMV DNA in plasma. The results suggest that antiviral resistance should be considered when selecting therapy for CMV CNS disease that develops in patients receiving treatment for CMV retinitis. In addition, plasma CMV DNA in AIDS patients receiving anti-CMV therapy may be a useful marker of disease progression and antiviral resistance.