The aim of this study was to evaluate the efficacy of pre-emptive antiviral therapy, based on a semi-quantitative nested PCR for cytomegalovirus (CMV) DNA in leukocytes, for the prevention of CMV disease after allogeneic BMT. Fifty-eight patients were prospectively followed with PCR for CMV DNA and antiviral therapy with ganciclovir was initiated after two consecutive positive tests. The levels of CMV DNA were determined by serial dilutions of the positive samples. The probability of detection of CMV DNA was 48.3% and the probability of CMV disease 6% at 100 days after BMT. Patients with CMV disease had higher CMV DNA levels compared with patients without CMV disease (P = 0.001). In comparison to 58 matched historical controls detection of CMV DNA was 5 days earlier (NS) and antiviral therapy could be initiated 10 days earlier in patients followed by PCR (P = 0.05). Pre-emptive antiviral therapy was given to 28 patients in a total of 36 courses. Patients became negative in PCR after 28 of 36 courses (77%). We conclude that PCR for CMV DNA can be used for early detection of CMV infection and as the basis of initiation of pre-emptive antiviral therapy in BMT patients.