Cytomegalovirus (CMV) UL97 mutations associated with ganciclovir resistance at codons 460, 594, and 595 were detected by polymerase chain reaction (PCR) followed by restriction enzyme analysis in CMV blood isolates and directly in polymorphonuclear leukocyte (PMNL) DNA extracts of 4 subjects who died of progressive disseminated CMV disease due to ganciclovir-resistant CMV strains. The CMV DNA load was also serially determined in leukocyte fractions of these patients using a quantitative-competitive PCR assay. There was excellent concordance between specific UL97 mutations in blood culture isolates and those detected in PMNL fractions for all patients. Emergence of such UL97 mutations during ganciclovir therapy was associated with an increasing CMV DNA burden in leukocytes of the 2 patients with AIDS but not in the 2 subjects with chronic lymphocytic leukemia. Rapid molecular strategies, including detection of common CMV UL97 mutations and CMV DNA quantitation, can be used directly in leukocytes of immunocompromised subjects with CMV disease to monitor antiviral therapy.