The HealthRise initiative seeks to implement and evaluate innovative community-based strategies for diabetes, hypertension and hypercholesterolemia along the entire continuum of care (CoC)-from awareness and diagnosis, through treatment and control. In this study, we present baseline findings from HealthRise South Africa, identifying gaps in the CoC, as well as key barriers to care for non-communicable diseases (NCDs). This mixed-methods needs assessment utilized national household data, health facility surveys, focus group discussions, and key informant interviews in Umgungundlovu and Pixley ka Seme districts. Risk factor and disease prevalence were estimated from the South Africa National Health and Nutrition Examination Survey. Health facility surveys were conducted at 86 facilities, focusing on essential intervention, medications and standard treatment guidelines. Quantitative results are presented descriptively, and qualitative data was analyzed using a framework approach. 46.8% of the population in Umgungundlovu and 51.0% in Pixley ka Seme were hypertensive. Diabetes was present in 11.0% and 9.7% of the population in Umgungundlovu and Pixley ka Seme. Hypercholesterolemia was more common in Pixley ka Seme (17.3% vs. 11.1%). Women and those of Indian descent were more likely to have diabetes. More than half of the population was found to be overweight, and binge drinking, inactivity and smoking were all common. More than half of patients with hypertension were unaware of their disease status (51.6% in Pixley ka Seme and 51.3% in Umgungundlovu), while the largest gap in the diabetes CoC occurred between initiation of treatment and achieving disease control. Demand-side barriers included lack of transportation, concerns about confidentiality, perceived discrimination and long wait times. Supply-side barriers included limited availability of testing equipment, inadequate staffing, and pharmaceutical stock outs. In this baseline assessment of two South African health districts we found high rates of undiagnosed hypercholesterolemia and hypertension, and poor control of hypercholesterolemia, hypertension, and diabetes. The HealthRise Initiative will need to address key supply- and demand-side barriers in an effort to improve important NCD outcomes.