Rectal squamous metaplasia in inflammatory bowel disease is rare. We present 2 cases of rectal squamous metaplasia, one in a patient with Crohn's disease and another with ulcerative colitis. Given the risk of malignant transformation, dysplasia surveillance is important particularly in areas of chronic inflammation. Furthermore, human papilloma virus (HPV) is involved in the pathogenesis of anal squamous cell carcinoma (SCC), but no guidelines exist in the United States for HPV prophylaxis against anal SCC in inflammatory bowel disease. HPV vaccination should be considered in high-risk patients younger than 45 years for prevention of anal SCC, including those with rectal squamous metaplasia.