HIV-1 variation was examined in a longitudinal phylogenetic analysis of the V3 region of the HIV env gene in 8 hemophiliac children and adolescents. The patients were selected based on the rate of CD4 T- cell decline during the first two years of enrollment in the Hemophilia Growth and Development Study. The analysis differs from most previous studies in that plasma HIV viral RNA and not proviral DNA was analyzed for the extent and character of virion diversity during the latent asymptomatic period through CD4 T-cell decline. Major preliminary findings are: (1) Individuals with similar clinical courses have distinctively different levels of viral diversity during the period of CD4 T-cell decline, suggesting differential immune pressures driving the rate of quasispecies evolution. (2) Two divergent populations of HIV in a single patient, one with macrophage- and the other T-cell-tropic genotypic features, co-existing over multiple timepoints and with different rates of evolution were detected. (3) Positive selection for amino acid substitution within the V3 region correlates well with immune status. In three of the four patients, there was a general trend towards positive selection for change when CD4 T-cell counts were >200, but mutations tend to be silent when immune pressure decreased as CD4 T-cell counts fell below 200. (4) Sequences from multiple timepoints within a patient did not cluster in distinct clades. Instead intra-timepoint sequences were found to overlap with sequences from other timepoints. This suggests that early variants persist over time and may represent escape mutants that evaded immune surveillance.