Antiviral susceptibility testing-flow cytometric analysis (AST-FCA), an application of flow cytometry in conjunction with cell culture, was developed to identify susceptibility of cytomegalovirus (CMV) isolates to the antiviral drugs ganciclovir (GCV) and foscarnet (PFA). The viral isolates used in this study were obtained from peripheral blood of AIDS patients. Among GCV-susceptible strains, the mean 50% inhibitory concentration (IC50) using AST-FCA was 18 microns (SI50 = 1.4). Among GCV resistant strains, the mean IC50 was 47 microns (SI50 = 3.6). For PFA, the mean IC50 was 80 microns (SI50 = 1.0) for susceptible strains. IC50s for strains resistant to PFA, showed no significant reduction of infectivity at the highest drug concentration (i.e., 200 microns PFA) tested. Additional analyses confirmed the accuracy of AST-FCA by parallel testing using plaque reduction assay. AST-FCA is a novel, nonisotopic, and relatively simple to perform laboratory procedure for the identification of CMV drug-resistant strains.