BackgroundLittle is known about the clinical presentation and outcomes amongst older HIV infected populations accessing ART in sub-Saharan Africa. We compared mortality amongst HIV infected patients accessing ART that were <  50 years to those ≥50 years in Kwa-Zulu Natal, South Africa.MethodsWe undertook a retrospective review of medical records of patients that accessed HIV services at the CAPRISA AIDS Treatment program (CAT) between June 2004 to December 2012 (N = 4003). HIV infected patients, 14 years or older were enrolled. All-cause mortality and treatment response to ART in those < 50 years to those ≥50 years were compared. A Kaplan-Meier curve and log-rank test were used to compare the cumulative probability of death between the two age groups with the primary endpoint being mortality. Statistical analysis was done using SAS (version 9.4.; SAS Institute Inc., Cary, NC, USA).ResultsOf 4003 individuals, 262 (6.5%) were ≥ 50 years (older group). The median age in those ≥50 years and <  50 year was 54.5 and 32.0 years, respectively. The younger group was mainly female (64.7%). There was no difference in mortality rate, between the older (6.9/100 person-years (py), 95% confidence interval (CI): 4.7–9.6) and younger group (5.3/100 py, 95% CI: 4.7–5.8) at 60 months (p = 0.137). In the multivariable model older patients had a significantly higher risk of death compared to younger patients. (hazard ratio (HR) 1.60, 95% CI: 1.08–2.39, p = 0.019).The rate of CD4+ cell count increase was higher in those < 50 years (β = 0.34, 95% CI: 0.19–0.50, p < 0.001) with no difference in viral suppression. The older group showed significantly higher prevalence of diabetes (6.3%) and hypertension (21.5%), p < 0.001.ConclusionART initiation in older HIV infected patients was associated with a higher mortality compared to those younger than 50 years. ART immunological response was less robust in older individuals. The increase in hypertension and diabetes among older patients suggests the need to restructure and integrate primary and specialized health care services into ART services.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3083-z) contains supplementary material, which is available to authorized users.