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Evaluations of CD4 cell count and other prognostic factors on the survival of HIV patients in sub-Saharan Africa are extremely limited. Funders have been reticent to recommend earlier initiation of treatment. We aimed to examine the effect of baseline CD4 cell count on mortality using data from HIV patients receiving combination antiretroviral therapy (cART) in Uganda.Observational study of patients aged at least 14 years enrolled in 10 clinics across Uganda for which The AIDS Support Organization (TASO) has data.CD4 cell count was stratified into categories (<50, 50–99, 100–149, 150–199, 200–249, 250–299, ≥300 cells/μl) and Cox proportional hazards regression was used to model the associations between CD4 cell count and mortality.A total of 22 315 patients were included. 1498 patients died during follow-up (6.7%) and 1433 (6.4%) of patients were lost to follow-up. Crude mortality rates (CMRs) ranged from 53.8 per 1000 patient-years [95% confidence interval (CI) 48.8–58.8] among those with CD4 cell counts of less than 50, to 15.7, (95% CI 12.1–19.3) among those with at least 300 cells/μl. Relative to a baseline CD4 cell count of less than 50 cells/μl, the risk of mortality was 0.75 (95% CI 0.65–0.88), 0.60 (95% CI 0.51–0.70), 0.43 (0.37–0.50), and 0.41 (0.33–0.51) for those with baseline CD4 cell counts of 50–99, 100–149, 150–249, and ≥250 cells/μl, respectively.Earlier initiation of cART is associated with increased survival benefits over deferred treatment.