Objective: To establish human immunodeficiency virus type 1 (HIV-1) messenger RNA (mRNA) expression in peripheral blood mononuclear cells as a marker of risk for progression to the acquired immunodeficiency syndrome (AIDS) in a large cohort of HIV-infected persons followed for a prolonged period. Design: Retrospective testing of cryopreserved, coded specimens. Setting: Research laboratories at the New York Blood Center and the Rockefeller University. Patients: 150 homosexual men infected with HIV-I who did not have an AIDS diagnosis at the time of testing. Measurements: Multiply spliced and unspliced HIV-I mRNAs in total peripheral blood mononuclear cell RNA were quantitated using reverse transcriptase-initiated polymerase chain reaction (PCR) and compared with other laboratory data and clinical outcome during the subsequent 8 years. Results: Although HIV-1 mRNA expression generally correlated with immunologic status, it was associated with future disease progression independently of CD4(+) cell counts or their rate of decrease at the time of sampling. The association of HIV-1 mRNA with disease progression in persons with CD4(+) cell counts higher than the median (>624 cells/mm(3)) was particularly noteworthy; further variation in the CD4(+) cell counts within this group was not prognostically significant. Conclusions: The expression of HIV-1 mRNA in peripheral blood mononuclear cells is a strong independent marker for future HIV disease progression, even in persons with normal T-cell subsets.