Bronchoalveolar lavage (BAL) fluids and serum samples from 153 patients with pulmonary symptoms who were infected with human immunodeficiency virus (HIV) and underwent BAL were examined for the presence of cytomegalovirus (CMV) by conventional culture and by polymerase chain reaction (PCR) for detection of CMV DNA. PCR detected CMV more frequently than did cultures of BAL fluid (PCR of BAL fluid, 53%; PCR of serum, 40%; and culture, 30%). In a multivariate model, development of extrapulmonary CMV disease was predicted by the finding of CMV in BAL fluid by culture (relative risk [RR], 8.0; confidence interval [CI], 3.8-16.8) or the finding of CMV DNA in serum (RR, 7.4; CI, 3.2-17.3) or BAL fluid (RR, 8.0; CI, 3.1-20.7) by PCR. Mortality was found to be similar for patients who did or did not have CMV detected by either culture or PCR. Detection of CMV DNA by PCR was a more rapid and sensitive technique than conventional culture. Detection of CMV DNA in BAL fluid or serum predicted subsequent development of extrapulmonary CMV disease but not death for HIV-infected patients with pulmonary symptoms.