Purpose: Anorectal function of inflammatory bowel disease (IBD) patients is still poorly understood, with contradictory results. This prospective observational study aimed to analyze the effect of perianal disease on anorectal function and quality of life in IBD patients. Methods: Patient assessment included full clinical examination, validated scores, anorectal manometry, three-dimensional endoanal ultrasonography, and endoscopy. The Inflammatory Bowel Disease Questionnaire was adopted to evaluate patients' quality of life. Results: From January to November 2016, 37 consecutive IBD patients (30 Crohn's disease, 7 ulcerative colitis) and 20 controls were enrolled in the study. Twenty-five patients had a history of perianal fistula, 9 reported fecal incontinence, and 2 had anal fissure. Fecal incontinent patients were older, had a longer disease duration, and higher bowel movement number than continent patients. Endoanal ultrasound findings were normal in all volunteers, while pathological features were found in 31/37 patients. Rectal sensory testing and anal pressure did not differ between the IBD patients and controls. However, the rectoanal inhibitory reflex was normally elicited in all controls vs. 32/37 (86%) IBD patients; 25/37 (68%) IBD patients showed manometric features of dyssynergic defecation. Rectal inflammation and incontinence were associated with low maximum anal resting pressure. The quality of life score was lower in ulcerative colitis patients than in Crohn's patients and significantly lower in fecal incontinent patients. Conclusions: Anorectal function is impaired in IBD patients with perianal disease. Fecal incontinence correlates with poorer quality of life. Anorectal manometry and ultrasonography are useful tools for evaluating IBD patients.