Patients with inflammatory bowel diseases often undergo surgical procedures for medically refractory disease or colitis associated dysplasia. Endoscopic evaluation of the surgically altered bowel is often needed to assess for disease recurrence, its severity, and for therapy. It is important to obtain and review the operative report and abdominal imaging before performing the endoscopy. Diagnostic and therapeutic endoscopy can be safely performed in most patients with inflammatory bowel disease with altered bowel anatomy under conscious sedation without fluoroscopy. Carefully planned stricture therapy with balloon dilation or needle knife stricturotomy can be performed for simple, short, and fibrotic strictures. A multidisciplinary approach involving a team of endoscopist, endoscopy nurse, colorectal surgeon, gastrointestinal pathologist, and gastrointestinal radiologist is important for a safe and effective endoscopy. We attempt to review the aspects that need consideration before the endoscopy, the technique of endoscopy, and briefly the therapies that can be performed during endoscopy of the bowel through an ileostomy, a colostomy, in the diverted large bowel or ileal pouch, and small bowel after stricturoplasty and bowel bypass surgery in patients with inflammatory bowel diseases.