Background The place of virtual colonoscopy (VC) in patients with Crohn's disease (CD) requiring endoscopic follow-up after surgery is unknown. The authors compared findings from VC versus conventional colonoscopy (CC) for assessing the postoperative recurrence of CD. Methods Sixteen patients with ileocolonic anastomosis for CD were prospectively enrolled from January 2001 to January 2002. Recurrence was assessed by CC according to Rutgeerts et al. VC was performed with a computed tomography scanner, with images examined by three radiologists who were unaware of the endoscopic findings. Results CC showed perianastomotic recurrence in 15 of 16 patients. Perianastomotic narrowing or stenosis was detected by VC in 11 of these 15 patients. There were 11 true positive, 1 true negative, 0 false-positive, and 4 false-negative findings (73% sensitivity, 100% specificity, 100% positive predictive value, 20% negative predictive value, 75% accuracy). Among the eight patients showing a rigid stenosis of the anastomosis not allowing passage of the colonoscope, VC detected narrowing or stenosis in seven patients. Conclusions The current findings suggest that although the widespread use of VC in CD is currently not indicated because of possible false-negative findings, this technique may represent an alternative to CC in noncompliant postsurgical patients with a rigid stenosis not allowing passage of the endoscope.