This in-vivo study was carried out to investigate alterations in the levels of proteins and enzymes produced by the liver of HIV infected pregnant women and HIV infected non pregnant women under different antiretroviral therapy. Forty six human patients (Pregnant patient, n=21, Non pregnant patient, n=25) were recruited during this study from the PEPFAR (President Bush Emergency Plan for Aids Research) clinic in LUTH (Lagos University teaching Hospital), Lagos. The patients were between the ages of 29 – 34 years. All samples were analyzed for Albumin, Transferrin, Urea, Total protein, Total bilirubin, Creatinine and Cholinesterase. Along with it, liver enzymes – Alkaline phosphate, Alanine aminotransferases and Aspartate aminotransferases were also analyzed to confirm proper liver function for each patient. Result showed that total bilirubin and transferrin were statistically higher in the pregnant group while other liver proteins (Albumin, Urea and Total protein) were statistically lower in the pregnant group. Two liver enzymes, Creatinine and Cholinesterase, were statistically lower in the pregnant group. Though, other liver enzymes; aspartate aminotransferases and alanine aminotransferases were also lower in the pregnant group. No significant difference were noted when statistics were applied. Only alkaline phosphatase showed a non significant increase in the pregnant group. Findings in this study suggest that effective antiretroviral therapy stabilizes proteins and enzymes production in both HIV groups, however, slight alterations which were observed in the pregnant HIV group were due to physiological changes during pregnancy.