Abstract: Highly Active Antiretroviral Therapy (HAART) has been associated with the development of a clinical group and metabolic disorders in AIDS. The aim of this study was to analyse the lipid profile, of HIV-1 infected individuals treated with or without Protease Inhibitor (PI) during the highly active antiretroviral therapy. A retrospective study was carried out on 40 healthy individuals (Control Group), 36 HIV-1 infected individuals not following antiretroviral therapy and 65 HIV-1 infected patients on antiviral therapy. The different HAARTs comprised: Lamivudin+Zidovudin+Indinavir (n = 10), Lamivudin+Zidovudin +Nevirapin (n = 7), Lamivudin+Zidovudin+Efavirenz (n = 7), Stavudin+Lamivudin+Efavirenz (n = 12) and Stavudin+Lamivudin+Nevirapin (n = 29). The duration of the antiviral therapy was comprised between 9 and 12 months. There were no differences between HAARTs in relation to the triglyceride and LDL cholesterol levels. The association of a protease inhibitor [Indinavir] with Zidovudin and Lamivudin induced a significant increase of total cholesterol compare to HIV negative as well as the LDL: HDL and total cholesterol: HDL ratios than in others HAARTs. The use of Efavirenz as Non Nucleotidic Reverse Transcriptase Inhibitor (NNRTI) was associated with elevated triglyceride levels while nevirapin increase the total cholesterol and both LDL and HDL cholesterol levels but a great improvement in LDL: HDL and cholesterol: HDL ratios was observed with the combination of Stavudin and lamivudin with Nevirapin compare to Efavirenz. The use of a protease inhibitor as well as Efavirenz in a combination therapy increased risk for coronary artery disease.