Lymphocytic alveolitis portends a poor prognosis in human immunodeficiency virus (HIV)-infected subjects. Because alveolar lymphocytes consist predominantly of HIV-specific CD8(+) cytotoxic T lymphocytes (CTL), they could represent an appropriate immune response to infected cells in the lung, and be a surrogate marker for a high pulmonary viral burden. We assessed long-term outcome in a cohort of asymptomatic HIV-infected subjects who underwent bronchoscopy between 1990 and 1993 and had bronchoalveolar lavage fluid (BALF) available for determination of viral load by reverse transcription-polymerase chain reaction. The ability to detect HIV in BALF increased with disease progression. Lymphocytic alveolitis, although present at all stages of HIV infection, was most pronounced in patients with middle stage disease. The HIV viral load as measured by bronchoalveolar lavage correlated with the percentage of alveolar lymphocytes in patients with peripheral blood CD4(+) cell counts above 200/microliter. Including patients with CD4(+) cell counts < 200/microliter weakened this correlation, possibly because of replacement of CD8(+) CTL by CD8(+) suppressor cells in advanced disease. Free virus in BALF was a stronger predictor of HIV disease progression than was lymphocytic alveolitis. These data suggest that lymphocytic alveolitis in HIV-infected subjects occurs in response to viral antigens in the lung and that the poor prognosis associated with lymphocytic alveolitis reflects a high pulmonary viral burden.