Infection with human immunodeficiency virus (HIV) causes a dysregulation of the immune system. This is caused by HIV-specific as well as non-specific mechanisms and has not been explained fully. In particular, knowledge is lacking about the potential role of host-mediated immunosuppressive mechanisms. During recent years it has become evident that a subpopulation of T cells [T regulatory (Tregs)] play a major role in sustaining tolerance to self-antigens. To investigate the influence of initiation of highly active anti-retroviral therapy (HAART) on the Treg level in HIV-infected patients we have conducted a prospective study enrolling treatment-naive HIV-infected patients just prior to starting treatment with HAART, measuring levels of Tregs by flow cytometry and mRNA expression of forkhead box P3 (FoxP3) at weeks 0, 4, 12 and 24 of treatment. In this prospective study neither the percentage of CD4+CD25high+ nor the expression of FoxP3 changed significantly during 24 weeks of HAART. Furthermore, HIV patients have higher Tregs measured as percentages of CD4+CD25high+ cells paralleled by higher levels of FoxP3 compared with healthy controls. The elevated level of Tregs was found to be independent of both immunological and virological status, indicating that initiation of HAART has minor effects on the Treg level in HIV-infected patients.