ABSTRACT Regulatory T cells (Tregs) are CD4+ T lymphocytes that express the gene FOXP3 and suppress other cellular immune responses. Their role in HIV pathogenesis is uncertain. Regulatory T cell (Treg) levels were analysed in peripheral blood of HIV infected patients and controls in South Africa. Immunophenotypic analysis revealed significantly elevated levels of FOXP3 positive Tregs in HIV infected patients (median 6.8%) compared with controls (median 3.7%). Treg levels were inversely correlated with CD4+ T cell count. FOXP3 mRNA expression was dependent on choice of reference gene (GAPDH or 18sRNA) and did not correlate with FOXP3 protein expression analysed flow cytometrically. These findings illustrate that Tregs are elevated in the peripheral blood of patients with late stage HIV disease and suggest a role for Tregs in the clinical immune suppression seen in these patients. Tregs may prove to be useful therapeutic targets for intervention or as a prognostic monitoring tool.