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Objective: HIV positive individuals infected with viral hepatitis B (HBV) or C (HCV) are at an increased risk of progression to kidney and liver failures. Therefore, prior to initiation of antiretroviral therapy, early diagnosis and initiation of appropriate treatment protocols are imperative for co-infected individuals. This study evaluated the prevalence of HBV and HCV, and extent of liver and renal dysfunction among 90 newly diagnosed HIV patients attending the Cape Coast Teaching Hospital HIV clinic., Results: Levels of alanine aminotransferase, aspartate-platelet ratio index and estimated glomerular filtration rate were used respectively to diagnose hepatotoxicity, liver fibrosis and chronic kidney disease (CKD). Association analyses were evaluated by Pearson's Chi-square test or Fisher's exact test and considered significant at p < 0.05. Using rapid diagnostic tests, 75.6% (n = 68) had HIV1 mono-infection, 24.4% (n = 22) had HIV1/HBV co-infection while 0.0% (n = 0) had HIV1/HCV co-infection. The prevalence of hepatotoxicity, liver fibrosis, and CKD were 7.8% (n = 7), 2.2% (n = 2), and 15.5% (n = 14) respectively. Similar proportions of HIV1/HBV and HIV1 were diagnosed with liver fibrosis (p = 0.431). In relation to hepatotoxicity Grade, a high proportion of HIV1/HBV were diagnosed with Grade 2 (p = 0.042). Also, severely reduced kidney function (CKD stage 4) was observed in only HIV1/HBV (n = 2, 9.1%, p = 0.053).