In order to compare PCR with rapid virus culture for the early detection of CMV in bronchoalveolar lavage (BAL) after bone marrow transplantation, 26 asymptomatic patients were routinely evaluated for the presence of CMV on day 35 using these two techniques. Concurrent blood samples were also analyzed in all cases. CMV was detected synchronously by both culture and PCR in six of 26 (23%) BAL and in five of 26 (19%) blood specimens. Among these positive specimens, three BAL and blood samples were positive in the same patients. Five (19%) BAL and five (19%) blood samples were culture-negative but PCR-positive. No BAL or blood specimens were positive by culture alone. When considering matched BAL-blood samples, five were positive in only one fluid, BAL (n = 3) or blood (n = 2) using culture, while seven were positive in only one fluid, BAL (n = 4) or blood (in = 3) using PCR. Overall, six of 26 (23%) patients had culture-negative but PCR-positive results. Three of these six patients were positive only in BAL and two of them subsequently received antiviral therapy for development of symptoms suggestive of CMV infection. We suggest that asymptomatic patients with negative-culture but PCR-positive results on day 35 in BAL should be subsequently closely monitored for the presence of CMV.