Human Immuno-deficiency Virus (HIV) infection is associated with lipoprotein abnormalities leading to cardiovascular diseases. Few reports are available about plasma apoproteins concentration abnormalities and apolipoproteins genes mutations in HIV infected persons. This study aimed to investigate the association between lipoprotein abnormalities and the Apolipoprotein B100 gene Xba1 and EcoR1 polymorphisms in HIV infected patients. A total of 87 controls and 70 HIVinfected antiretroviral-naive patients were included. Their serum lipids and apolipoproteins profiles were determined. In subjects with dyslipidemia, the molecular characterization of the apolipoprotein B100 gene was carried out using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Total cholesterolemia (1.82±0.46 g/L or 4.70±1.2 mMol/L vs 1.97±0.44 g/L or 5.08±1.14 mMol/L) and apolipoproteinemia A1 (1200±0250 mg/L or 1.20±0.25 g/L vs 1430±240 mg/L or 1.43±0, 24g/L) were lower in HIV-positive (p=0.038 and 0.0001 respectively) but the atherogenic index ApoB100/ApoA1 (0.79±0.32 vs 0.69±0.22) was higher in HIV-positive (p=0.041). Apo B100 gene mutations related to both polymorphisms studied were found in the 2 groups. Hyperapolipoproteinemia B100 and normal LDL Cholesterolemia were predominant regardless of the polymorphism (Xba1 or Eco R1) and allele status (mutant or wild).HIV-positive patients were more at risk of cardiovascular diseases. The mutations of the ApoB100 gene have been found but their established relationship with dyslipoproteinemias is to be confirmed.