BACKGROUND: Historically, sub-Saharan Africa has reported low levels of atherosclerotic cardiovascular disease (CVD). However as these populations undergo epidemiological transition, this may change. METHODS: This was an observational cohort study performed at Chris Hani Baragwanath Hospital in Soweto, South Africa. As part of the Heart of Soweto study, a clinical registry captured detailed clinical data on all de novo cases of structural and functional heart disease presenting to the Cardiology unit during the period 2006 to 2008. We examined fasting lipid profiles in 2 182 patients (of 5 328 total cases) according to self-reported ethnicity. The study cohort comprised 1 823 patients of African descent (61% female, aged 56 ± 16 years), 142 white Europeans (36% female, aged 57 ± 13 years), 133 Indians (51% female, aged 59 ± 12 years) and 87 of mixed ancestry (40% female, aged 56 ± 12 years). RESULTS: Consistent with different patterns in heart disease aetiology, there were clear differences in total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglycerides across ethnicities (p < 0.001): patients of African descent had the lowest TC and LDL-C levels and Indians the highest. However, there were no significant differences in high-density lipoprotein cholesterol (HDL-C) levels between ethnicities (p = 0.20). Adjusting for age, gender and body mass index, patients of African descent were significantly less likely to record a TC of > 4.5 mmol/l (OR 0.33, 95% CI: 0.25-0.41) compared to all ethnic groups (all p < 0.001). CONCLUSIONS: These data confirm important blood lipid differentials according to ethnicity in patients diagnosed with heart disease in Soweto, South Africa. Such disparities in CVD risk factors may justify the use of specialised prevention and management protocols.