Restriction endonuclease analysis of purified viral DNA was used to study the molecular epidemiologic characteristics of cytomegalovirus infection in 18 patients having bone marrow transplantation. Four patients who had had asymptomatic excretion of cytomegalovirus in urine before transplantation subsequently developed a cytomegalovirus infection after transplantation (pneumonia in 2 patients, fever and viremia in 1 patient, and asymptomatic viruria in 1 patient). In each patient, the infection that developed after transplantation was caused by a cytomegalovirus strain genetically identical to the isolate detected in urine before transplantation. Cytomegalovirus isolates from different sites (buffy coat, lung, and urine) of the same patient were also identical, but cytomegalovirus isolates from different patients were never identical. Our results suggest that some cytomegalovirus infections after bone marrow transplantation may be caused by strains present before transplantation. The great structural and genetic variability of cytomegalovirus isolates must be considered in the development of effective diagnostic and immunoprophylactic measures for infection after marrow transplantation.