Chlamydia pneumoniae has now been associated with pneumonia, bronchitis, pharyngitis, acute chest syndrome of sickle cell disease, and asthma. Because of the difficulty of primary isolation and tissue-culture adaptation of this organism, we used a previously developed polymerase chain reaction-enzyme immunoassay (PCR-EIA) to screen 132 culture-negative bronchoalveolar lavage (BAL) specimens from 108 immunocompromised patients (34% of whom were positive for human immunodeficiency virus) and 7 healthy volunteers. Thirteen specimens (9.8%) from 12 immunocompromised patients (11.1%) gave a positive result; one patient had two positive specimens obtained 3 days apart. No healthy volunteer had a PCR-EIA-positive BAL specimen. Twelve (11.1%) of the immunocompromised patients also had diagnostic levels of antibody. Four patients had positive results in both PCR-EIA and serological tests. Thus 20 (18.5%) of the 108 patients had laboratory evidence of C. pneumoniae infection. These data indicate that diagnosis of acute infection with C. pneumoniae can be established more rapidly and reliably by PCR-EIA than by culture or serology, particularly among immunocompromised patients, in whom serological changes in response to infection are relatively undependable. With an infection rate of 11.1% according to PCR-EIA, C. pneumoniae should be considered in the evaluation and treatment of pneumonia in immunocompromised patients.