Abnormalities in pulmonary function tests have been observed in AIDS patients with pulmonary disease. In this study, the polymerase chain reaction (PCR) was used to determine if the reductions in transfer factor for lung carbon monoxide (TLCO) were due to the presence of HIV-1 or cytomegalovirus (CMV). HIV-1 was detected in cells from bronchoalveolar lavage (BAL) in 35 out of 60 (58%) of patients. The detection of HIV-1 had no significant effect on pulmonary function. CMV was detected in the BAL of 58% of patients in this study but CMV was the sole viral pathogen in the lung of only two out of 60 (3.3%) individuals. A significant reduction in TLCO was observed in individuals with PCP where CMV was also detected in the BAL. This study shows that reduction in TLCO in HIV-seropositive patients is not due to the presence of HIV-1 or CMV alone in BAL cells.