The objectives of this study was to estimate the risk of anal incontinence in morbidly obese women and to identify risk factors associated with anal incontinence in an obese population sample. A case-control study based on the registry of a university hospital obesity unit. A consecutive sample of women with body mass index > or = 35 (obesity class II) was randomly matched by age, gender and residential county to control subjects using the computerised Register of the Total Population. Data were collected by a self-reported postal survey including detailed questions on medical and obstetrical history, obesity history, socioeconomic indices, life style factors and the validated Cleveland Clinic Incontinence Score. The questionnaire was returned by 131/179 (73%) of the cases and 453/892 (51%) of the control subjects. Compared to the control group, obese women reported a significantly increased defecation frequency (p < 0.001), inability to discriminate between flatus and faeces (p < 0.001) and flatus incontinence (p < 0.001). Compared with non-obese women, the adjusted odds ratio (OR) for flatus incontinence in morbidly obese women was 1.5 [95% confidence interval (CI) 1.1-4.1]. A history of obstetric sphincter injury was independently associated with an increased risk of flatus incontinence (OR, 4.3; 95% CI, 2.0-9.2) and incontinence of loose stools (OR, 6.6; 95% CI, 1.4-31.4). Other medical and life style interactions did not remain at significant levels in an adjusted multivariable analysis. Obese women are at increased risk for mild to moderate flatus incontinence.