Background Obesity is a major risk factor for emerging non-communicable diseases (NCDS) in middle income countries including South Africa (SA). Understanding the multiple and complex determinants of obesity and their true population attributable impact is critical for informing and developing effective prevention efforts using scientific based evidence. This study identified contextualised high impact factors associated with obesity in South Africa. Methods Analysis of three national cross sectional (repeated panel) surveys, using a multilevel logistic regression and population attributable fraction estimation allowed for identification of contextualised high impact factors associated with obesity (BMI>30 kg/m2) among adults (15years+). Results Obesity prevalence increased significantly from 23.5% in 2008 to 27.2% in 2012, with a significantly (p-value<0.001) higher prevalence among females (37.9% in 2012) compared to males (13.3% in 2012). Living in formal urban areas, white ethnicity, being married, not exercising and/or in higher socio-economic category were significantly associated with male obesity. Females living in formal or informal urban areas, higher crime areas, African/White ethnicity, married, not exercising, in a higher socio-economic category and/or living in households with proportionate higher spending on food (and unhealthy food options) were significantly more likely to be obese. The identified determinants appeared to account for 75% and 43% of male and female obesity respectively. White males had the highest relative gain in obesity from 2008 to 2012. Conclusions The rising prevalence of obesity in South Africa is significant and over the past 5 years the rising prevalence of Type-2 diabetes has mirrored this pattern, especially among females. Targeting young adolescent girls should be a priority. Addressing determinants of obesity will involve a multifaceted strategy and requires at individual and population levels. With rising costs in the private and public sector to combat obesity related NCDS, this analysis can inform culturally sensitive mass communications and wellness campaigns. Knowledge of social determinants is critical to develop “best buys”.