HIV-related anemia is associated with increased risk of death. Prior studies suggest an inverse relationship between CD4 cell count and anemia, and a positive relationship between HIV-clinical stage and anemia. However, none have assessed the role of antiretroviral therapy (ART) treatment combinations in these relationships. Therefore, we conducted a cross-sectional study to evaluate the relationship between CD4 cell count, HIV clinical stage and anemia among 4803 Ugandan HIV-patients, and assessed the role of ART treatment combinations. We included HIV patients (> 15 years) receiving ART therapy combinations between 2010- 2015. We evaluated CD4 cell count and anemia using blood tests, and HIV-clinical staging was based upon the World Health Organization HIV-clinical staging system. Information on ART treatment combinations was obtained from patients’ medical records. Multinomial logistic regression was used to model the relationship between CD4 cell count, HIV clinical stages and anemia. We performed a sensitivity analysis to examine the role of ART treatment combinations. The odds of being severely anemic were highest among those classified in the low CD4 cell count category (<200cells/μL), and those at WHO stage IV. Odds Ratios were 3.7 (95% CI; 1.48-9.26) and 3.2 (95% CI; 1.75-5.70), respectively. Stratification by ART treatment combinations (TDF-based versus ADZ-based combination treatment) indicated an increase in the odds of being anemic with increase in HIV-clinical stage (stage II, OR: 1.99, 95% CI; 1.44-2.78; stage III, OR:3.17, 95% CI; 2.21-4.54, & stage IV, OR; 4.42, 95% CI; 2.68-7.30), for individuals receiving TDF-based treatment only. Results suggest that HIV-patients with a low CD4 cell count and, those in advanced HIV-clinical stages should consider regular hemoglobin follow-up to identify and treat anemia at its earliest stages.