Autoantibodies appear in the sera of rhesus macaques following SIV infection. The present study was conducted to examine the role of viral load, antiviral chemotherapy and stage of disease on the titers of such autoantibodies and the spectrum of autoantigens that become the target of such autoimmune responses. In addition, the role of regulatory T cells (Tregs) was also examined. Results of these studies showed that the highest autoantibody titers were noted in animals with lower relative plasma viral loads with a wider spectrum of autoantigens that are the target of such responses as compared with lower autoantibody titers in animals with relatively higher plasma viral loads and a narrower spectrum of autoantigens. Short-term antiviral chemotherapy did not influence the titers of autoantibodies. While there was a gradual decrease in the frequency and absolute number of Tregs, the levels of Tregs was inversely correlated with viral load and lower autoantibody titers. The mechanisms for these differences remain unknown and suggest complex relationships exist between levels of immunosuppression, autoimmune response, homeostatic proliferation and the spectrum of autoantigens that become the target of such autoimmune responses.