Duodenal obstruction is a classic complication of Crohn's disease with duodenal involvement. However, malignant transformation of duodenal lesions has very rarely been reported, and diagnosis of such a transformation is rarely made preoperatively. We report the case of a 32-year-old patient with an 8-year history of Crohn's disease who underwent bypass gastrojejunostomy for a duodenal stricture. A year later, weight loss and biliary obstruction led to a further laparotomy. At operation, an advanced carcinoma with peritoneal seedings was confirmed. Of the three patients previously reported in the literature with duodenal cancer arising in Crohn's disease stricture, only one had a preoperative diagnosis of malignancy made from endoscopic biopsies. When considering the surgical bypass of Crohn's duodenal stricture, if preoperative endoscopy and biopsy cannot be performed on account of duodenal stricturing, we suggest performing a peroperative endoscopy via a jejunotomy in order to eliminate the diagnosis of associated duodenal malignancy.