Fecal incontinence (FI) and urgency are prevalent symptoms in patients with inflammatory bowel diseases (IBD). It is unclear which factors determine their severity. We evaluated associations of clinical activity, anorectal motility, and endoanal sonography with FI severity in IBD. Fifty-eight consecutive IBD patients and 14 healthy volunteers participated in a cross-sectional, tertiary-center study. Active disease was defined as Crohn's disease activity index ≥ 150 and as simple clinical colitis index > 2. We assessed anal pressures and fatigue rate index (FRI) of the external anal sphincter (EAS) by manometry, rectal compliance and sensitivity by balloon distension, and sphincter defects by endoanal ultrasound. Significant bivariate associations between these parameters and the fecal incontinence severity scale (FISS) were evaluated in multivariate analysis. Twenty-seven patients (47%) reported urgency, 13 of which (22%) reported FI. Defects of the internal anal sphincter (IAS) and the EAS were diagnosed in 14 (24%) and 13 patients (22%), respectively. Patients had significantly lower rectal compliance and FRI compared with controls. FISS demonstrated significant bivariate associations with clinical disease activity (P = 0.0115), FRI (P = 0.0018), sonographic IAS and EAS defects (P < 0.0001 and 0.0059), rectal compliance (P = 0.0001), and volume at the threshold of a constant urge (Vurge, P = 0.0002). In multivariate analysis, FISS was associated with clinical disease activity (P = 0.0325), FRI (P = 0.0367), Vurge (P = 0.0091), and sonographic IAS defect(s) (P = 0.0008). The derived model explained 62% of the variance in FISS (P < 0.0001). Clinical disease activity and manometric and sonographic anorectal parameters are associated with FI severity in IBD. Prospective studies are warranted to evaluate their predictive value in continence outcomes.