Acquired immune deficiency syndrome, caused by the human immunodeficiency virus (HIV) is exemplified by progressive impaired body’s immune system resulting in a number of opportunistic infections and biochemical complications. The advent of HAART has enhanced opportunistic infections and increased quality of life of infected individuals. However, the long-term treatment with HAART is associated with substantial toxicity, adherence difficulties and drug resistance. The study purpose was to assess the long-term effect of HAART and anti-Tuberculosis on the key biochemical markers such as ALT, AST and GGT enzyme levels of the liver of HIV-TB co-infected patients in KCCA Kiswa health Centre III a case in Uganda.