Crohn’s disease manifests with perianal or rectal symptoms in approximately one-third of patients, and is associated with a more aggressive natural history. Due to the chronic relapsing nature of the disease, surgery has been traditionally avoided. However, combined medical and surgical intervention when treating perianal fistulae has been shown to offer the best chance for success. Endoanal ultrasound examination or pelvic magnetic resonance imaging should be done in conjunction with an examination under anesthesia to characterize the disease. Any abscess should be drained and setons placed if there is active rectal inflammation or complex fistulae. Antibiotics and immunosuppressive therapy (especially with infliximab) should also be initiated. Simple fistulae can be treated surgically by fistulotomy or anal fistula plug. Complex fistulae can be closed with either an anal fistula plug or covered with flaps. Up to 20% of patients anorectal Crohn’s disease require proctectomy for persistent and disabling disease.