BACKGROUND: Little is known about the incidence and clinical characteristics of newly diagnosed atrial fibrillation/flutter (AF) in urban Africans in epidemiological transition. METHODS: This observational cohort study was carried out in the Chris Hani Baragwanath Hospital in Soweto South Africa. A clinical registry captured detailed clinical data on all de novo cases of AF presenting to the Cardiology Unit during the period 2006-2008. RESULTS: Overall, 246 of 5328 cardiac cases (4.6%) presented with AF (estimated 5.6 cases/100 000 population/annum). Mean age was 59±18 years and the majority were of African descent (n=211, 86%) and/or female (n=150, 61%). Men were more than twice as likely to smoke (OR 2.88, 95% CI 1.92 to 4.04) than women, but women were twice as likely to be obese (OR 1.80, 95% CI 1.28 to 2.52) than men. Lone AF occurred in 22 (8.9%) cases, while concurrent valve disease and/or functional valvular abnormality occurred in 107 cases (44%). Overall, 171 cases (70%) presented with uncontrolled AF (ventricular rate >90 beats/min) with no sex-based differences. Common co-morbidities were any form of heart failure (56%) and rheumatic heart disease (21%). Women with AF were more likely to present with hypertensive heart failure (OR 2.37, 95% CI 1.24 to 4.54) but less likely to present with a dilated cardiomyopathy (OR 0.42, 95% CI 0.23 to 0.76) or coronary artery disease (OR 0.38, 95% CI 0.14 to 1.02) than men. Mean overall CHADS(2) score (in 195 non-rheumatic cases) was 1.51±0.91 and, despite a similar age profile, women had higher scores than men (1.73±0.94 vs 1.24±0.78; p<0.0001). CONCLUSIONS: These unique data suggest that urban Africans in Soweto develop AF at a relatively young age. Conventional strategies used to manage and treat AF need to be carefully evaluated in this setting.