For national antiretroviral therapy (ART) programs, the most important health system goals in reducing morbidity and mortality among HIV-infection patients are to initiate treatment as early as eligibility criteria allow and to achieve the highest possible long-term retention of patients on ART. In South Africa, cohort data have consistently found high attrition among ART patients, with the combined cumulative outcomes of death and loss to follow up averaging 25-40% over the first five years after ART initiation. Like many other middle income countries, South Africa also faces very high rates of non-communicable diseases (NCDs) and NCD risks. Despite this, there are virtually no studies looking at interactions between ART and NCDs, and none that have considered the effect of NCDs and NCD risk factors on achieving the second health system goal mentioned above: long term retention on ART.