BACKGROUND Cytomegalovirus (CMV) infection is a major complication in immunocompromised patients, such as those with leukemia, acquired immunodeficiency syndrome (AIDS) and allograft recipients. A sensitive and specific diagnostic procedure of CMV infection is required. The polymerase chain reaction (PCR) procedure has been demonstrated to be more sensitive than conventional virus isolation. However, CMV DNA can be detected in patients with latent or asymptomatic infections by PCR because of its extreme sensitivity. OBJECTIVES In this study, we used PCR and reverse transcription PCR (RT-PCR) to detect CMV DNA and mRNA in immunocompromised patients and evaluated the value of PCR and RT-PCR for diagnosis of active CMV infection. STUDY DESIGN We examined thirty immunocompromised children for CMV DNA using peripheral blood mononuclear cells (PBMC), polymorphonuclear leukocytes (PMNL). urine and throat swabs from October 1991 to March 1992. Eighteen of the patients had acute lymphoblastic leukemia, four had non-Hodgkin's lymphoma, two had Wilms' tumor and six were recipients of an allogeneic bone marrow transplantation. Four patients developed CMV-related clinical symptoms during the observation period: two patients with pneumonia and two patients with hepatitis. RESULTS CMV DNA was detected in four patients with clinical symptoms and in five patients without evidence of CMV infection. The incidence of CMV DNA was significantly higher in symptomatic patients than asymptomatic patients. CMV mRNA encoding the late antigen was detected by RT-PCR only in patients with clinical symptoms of CMV infection. CONCLUSIONS We concluded that detection of CMV DNA by PCR is of little clinical significance for distinguishing latent form active CMV infection. It is suggested that detection of CMV mRNA by RT-PCR is useful for diagnosis of active CMV infection.