Total proctocolectomy with ileal pouch-anal anastomosis is the surgical procedure of choice for patients with medically-refractory ulcerative colitis or ulcerative colitis with associated dysplasia. Although most patients after ileal pouch-anal anastomosis experience good functional outcomes, a number of complications may develop. Of the long-term complications, pouchitis is most common. Although most respond to antibiotic treatment, some patients develop chronic pouchitis, leading to substantial morbidity and occasionally pouch failure. In patients with pouchitis who are not responsive to conventional antimicrobial therapy, secondary causes of chronic pouchitis need to be considered, including Crohn's disease of the pouch. In recent years, more literature has become available regarding the medical management of chronic pouchitis and Crohn's disease of the pouch, including the use of newer biologic agents. We herein provide a concise review on inflammatory complications involving the ileal pouch, including a focused approach to diagnosis and medical management.