A sensitive method has been developed for the quantification of cytomegalic endothelial cells (CEC) in peripheral blood (PB) of patients with active cytomegalovirus (CMV) infections. The three subsequent key steps of this method are density centrifugation to enrich endothelial cells (EC) in the mononuclear cell (MNC) fraction, EC-specific staining, and fluorescence-activated cell sorting (FACS) of EC onto adhesion slides. The FACS method was compared with the conventional method of cytocentrifugation of the MNC fraction onto slides, followed by EC-specific staining. The main advantage of the additional steps for the isolation and quantification of CEC in PB by FACS is a 10-times-greater sensitivity than by cytocentrifugation of the MNC fraction alone. The recovery percentages of EC from whole blood were comparable for both methods. Recoveries of EC obtained after FACS were 53% ± 16.5%, (mean ± standard deviation), and recoveries of EC obtained after cytocentrifugation of the MNC fraction were 43% ± 4.3%. In patients with active CMV infection, 5 to 72 CEC were detected by FACS, equivalent to 0.8 to 9.0 CEC/ml of blood. With this method for isolation and quantification, the characterization of CEC in PB of patients with CMV-associated clinical symptoms, as well as the quantification of EC in PB of patients with pathophysiological manifestations involving endothelial damage that are different from those caused by CMV infections, can be performed.