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The impact of anal incontinence on women’s sexual function is poorly understood.The aim of this study was to investigate the relationship between anal incontinence and sexual activity and functioning in women.This is a cross-sectional study.This investigation was conducted in a community-based integrated health care delivery system.Included were 2269 ethnically diverse women aged 40 to 80 years.Self-administered questionnaires assessed accidental leakage of gas (flatal incontinence) and fluid/mucus/stool (fecal incontinence) in the past 3 months. Additional questionnaires assessed sexual activity, desire and satisfaction, as well as specific sexual problems (difficulty with arousal, lubrication, orgasm, or pain). Multivariable logistic regression models compared sexual function in women with 1) isolated flatal incontinence, 2) fecal incontinence (with or without flatal incontinence), and 3) no fecal/flatal incontinence, controlling for potential confounders.Twenty-four percent of women reported fecal incontinence and 43% reported isolated flatal incontinence in the previous 3 months. The majority were sexually active (62% of women without fecal/flatal incontinence, 66% with isolated flatal incontinence, and 60% with fecal incontinence; p = 0.06). In comparison with women without fecal/flatal incontinence, women with fecal incontinence were more likely to report low sexual desire (OR: 1.41 (CI: 1.10–1.82)), low sexual satisfaction (OR: 1.56 (CI: 1.14–2.12)), and limitation of sexual activity by physical health (OR: 1.65 (CI: 1.19–2.28)) after adjustment for confounders. Among sexually active women, women with fecal incontinence were more likely than women without fecal/flatal incontinence to report difficulties with lubrication (OR: 2.66 (CI: 1.76–4.00)), pain (OR: 2.44 (CI: 1.52–3.91)), and orgasm (OR: 1.68 (CI: 1.12–2.51)). Women with isolated flatal incontinence reported sexual functioning similar to women without fecal/flatal incontinence.The cross-sectional design prevented evaluation of causality.Although most women with fecal incontinence are at high risk for several aspects of sexual dysfunction, the presence of fecal incontinence does not prevent women from engaging in sexual activity. This indicates that sexual function is important to women with anal incontinence and should be prioritized during therapeutic management.