Vertical infection with human immunodeficiency virus-1 (HIV-1) causes profound changes in the proportions of subpopulations of lymphocytes in the peripheral circulation. In this study the percentages in whole blood of CD4 and CD8 cells, and of immunologically important subpopulations, were measured in 19 HIV-infected children over periods of up to 4 years and compared to our recently published ranges for normal children of various ages. The rate of CD4 decline and of CD8 increase differed between clinically fast and slow progressors. On CD8 cells, cytotoxic, memory (CD11abright and CD45R0), and activation (HLA-DR) markers were raised soon after birth to levels outside the normal range, and compared favorably with HIV culture as a method for early diagnosis of HIV infection. Mean levels of naive (CD45RA) and memory (CD45R0, CD29) markers on CD4 cells became significantly altered after 48 months of age, suggesting that these are markers of more advanced disease. Despite different ages of enrollment into the study, in the cohort as a whole, the levels of the lymphocyte subpopulations studied changed consistently. Thus, their measurement could be useful both in the diagnosis and prognosis of HIV infection in individual children. This is the first report showing that lymphocyte subpopulation analysis can play a major role in the diagnosis of pediatric HIV infection.