Cytomegalovirus (CMV) is a common cause of lower respiratory tract infections in immunocompromised individuals. Bronchoalveolar lavage (BAL) is a noninvasive means to procure large numbers of bronchial and alveolar cells from the lung. To assess various methods of detecting CMV in the lavage specimen, 26 BAL specimens from 16 patients at high risk for CMV infection were evaluated. The methods and time required for analysis were the following: cytologic examination of Papanicolaou-stained membrane filters (1 h); viral cytopathic effects in tissue culture (days to weeks); spin amplification followed by staining with a monoclonal antibody for detection of CMV early nuclear antigen (18 h); and in situ hybridization (IH) with a biotinylated complementary DNA (cDNA) CMV probe (5 h). CMV was detected in 11 of 26 (42%) specimens by the early antigen assay, ten of 26 (38%) by in situ hybridization, five of 26 (19%) by tissue culture, and three of 26 (12%) by routine cytology. The absence of diagnostic CMV nuclear and/or cytoplasmic inclusions in many specimens positive by in situ hybridization and/or early antigen detection assay may be in part due to low levels of viral replication, insufficient for the development of diagnostic inclusions. These data show that techniques using in situ hybridization or fluorescent anti-CMV antibodies are rapid and are more sensitive for CMV identification than both cytomorphological examination and traditional tissue culture methods. Additional studies are required to determine the clinical significance of early CMV detection by in situ hybridization and early nuclear antigen detection assays.