Multimorbidity in Sub-Saharan Africa is under researched and includes distinct disease combinations to those seen in high income countries. The aim of this study was to determine the prevalence and distribution of multimorbidity in South Africa, as well as the associated individual, area-level and contextual factors. Multilevel logistic regression analyses were conducted on nationally representative 2016 South Africa Demographic Health Survey Data. The sample included 5,342 individuals (level 1) who completed the Adult Health questionnaire living in 691 neighbourhoods (level 2) from nine provinces (level 3). Multimorbidity was present in 44.6% of the study population and ranged from
36.8% in Gauteng to 52.8% in Eastern Cape. Individuals who were older, women, formerly married, black, obese, consumed a medium amount of sugary drinks, received education to primary or secondary school level or exposed to smoke at work had an increased risk of multimorbidity. Province level factors including poverty, rurality and unemployment, as well as neighbourhood level poverty were associated with multimorbidity. Some evidence of residual multimorbidity clustering was observed at the neighbourhood but not province level. Therefore, strategies that aim to tackle multimorbidity should address the risk factors identified and the wider determinants of health within neighbourhoods.