To diagnose cytomegalovirus pneumonia in a hetergeneous population of patients, three methods for detection of CMV in bronchoalveolar lavage specimens were compared as follow: (1) spin amplification followed by staining with a monoclonal antibody to the early nuclear antigen (EA-assay); (2) conventional tissue cell culture; and (3) cytology. Cell differentials were performed on most specimens. Cytomegalovirus was detected by one or more method in 55 BAL specimens from 39 patients. Cytomegalovirus (CMV) pneumonia was diagnosed by lung tissue (primarily autopsy) histologic findings and conventional culture results or the presence of CMV in extrapulmonary tissue, fulfillment of specific clinical and radiographic criteria plus failure to recover a pathogen other than CMV from a respiratory specimen. Probable CMV pneumonia was diagnosed if only the latter two criteria were met. The EA-assay was positive in all patients with proven or probable CMV pneumonia and in 92 percent of those without documented pneumonia. Cytologic findings were positive only in patients with CMV pneumonia but were negative in one-third of those patients. As a diagnostic test for CMV pneumonia, the EA-assay, conventional culture, and cytology had positive predictive values of 45, 57, and 100 percent, respectively. Lymphocyte percentages in BAL specimens from patients with CMV pneumonia were significantly decreased compared with those of patients without CMV pneumonia (p less than 0.005). Although the EA-assay should not be used alone as a diagnostic test for CMV pneumonia in our patient population, the combination of alveolar lymphopenia and a positive BAL CMV EA-assay was highly suggestive of disease.