Purpose: The internal anal sphincter provides most of the resting anal tone and is the main muscle responseble for continence. This study was designed to estimate the prevalence of, and identify risk factors associated with, internal anal sphincter dysfunction in Japanese adults. Methods: Anorectal manometry was performed in 1193 women and 1124 men aged 20 years or older. The maximal resting pressure, measured by a rapid pull-through technique, was defined as the highest resting pressure recorded. Internal anal sphincter dysfunction was defined as a maximal resting pressure less than 30 mmHg. Potential risk factors were assessed through self-reports, interviews, physical examinations, and medical record reviews. Multivariate logistic regression analysis was used to identify independent risk factors for internal anal sphincter dysfunction. Results: Significant differences in maximal resting pressure were seen between women (58.1 ± 24.9 mmHg) and men (68.8 ± 23.5 mmHg, P < 0.001). Maximal resting pressure decreased significantly with increasing age in both sexes. The prevalence of internal anal sphincter dysfunction was 10.4% (15.5% in women, 5.1% in men). In a multivariate logistic regression model, age, mental disease, pelvic organ prolapse repair, and fecal incontinence were independently associated with a greater risk of internal anal sphincter dysfunction in women and men. Conclusions: Internal anal sphincter dysfunction is a common problem for women and men. Several of the identified risk factors are preventable or modifiable, and may direct future research in fecal incontinence therapy.