The advent of highly active antiretroviral therapy (HAART) has been effective in the treatment of AIDS patients. However, after receiving this treatment for various periods of time, there is in some patients a significant increase in plasma viral load without a decrease in CD4+ T cell count. Our study involved nine such AIDS patients showing this discordance. We characterized changes in the nef gene of plasma HIV-1 isolated from these patients. Viral RNA was extracted from patient plasma, amplified by RT-PCR, cloned, and sequenced. Three sequences from each patient were obtained. The sequences were aligned and compared with other strains of HIV-1. Various substitutions were seen in most patients; however, two patients showed unique insertions of different sizes that are probably due to HAART.