BACKGROUND: Health information systems for monitoring chronic non-communicable diseases (NCDs) in South Africa (SA) are relatively less advanced than those for infectious diseases (particularly tuberculosis and HIV) and for maternal and child health. NCDs are now the largest cause of premature mortality owing to exposure to risk factors arising from obesity that include physical inactivity and accessible, cheap but unhealthy diets. The National Strategic Plan for the Prevention and Control of Non-Communicable Diseases 2013 - 17 developed by the SA National Department of Health outlines targets and monitoring priorities. OBJECTIVES: To assess data sources relevant for monitoring NCDs and their risk factors by identifying the strengths and weaknesses, including usability and availability, of surveys and routine systems focusing at national and certain sub-national levels. METHODS: Publicly available survey and routine data sources were assessed for variables collected, their characteristics, frequency of data collection, geographical coverage and data availability. RESULTS: Survey data sources were found to be quite different in the way data variables are collected, their geographical coverage and also availability, while the main weakness of routine data sources was poor quality of data. CONCLUSIONS: To provide a sound basis for monitoring progress of NCDs and related risk factors, we recommend harmonising and strengthening available SA data sources in terms of data quality, definitions, categories used, timeliness, disease coverage and biomarker measurement.