Viral population diversity was assessed in samples collected from five HIV-infected women who were RNA positive and antibody negative. Similar to studies in men, highly conserved viral variants were detected (mean nucleotide diversity of 0.11% for p17p24, 0.32% for C2C3). In two individuals diversity was uncharacteristically lower in env C2C3 than in gag pl7p24, suggesting selection in env at this very early stage of infection.