BACKGROUND The aim was to evaluate and compare the diagnostic performance of magnetic resonance enteroclysis (MRE) and wireless video capsule endoscopy (CE) in detecting and classifying small bowel Crohn's disease (CD) proximal to the terminal ileum. METHODS Nineteen patients with histologically proven CD (M:F = 13:6; mean 34 years, range 17-65) were prospectively included in the study when presenting with clinical signs suggesting stricturing or inflammatory lesions of CD in the proximal small bowel. All patients underwent MRE with an infusion technique and were then admitted to CE. RESULTS As for the presence or absence of pathology, results of MRE and CE were in total agreement for 44/52 (85%) evaluated segments. In judging lesion severity, MRE and CE yielded identical results in 29/52 (56%) segments. MRE underestimated pathology in 7/52 (14%) segments and revealed more severe pathology in 6/52 (12%) segments. CE identified subtle (n = 7) or severe (n = 2) mucosal pathology while MRE was normal. CE entirely missed severe inflammatory mural changes depicted in MRE in 1/52 (2%) segments. CONCLUSIONS MRE and CE show good correlation in the detection and localization of inflammatory bowel disease. As for disease activity, MRE is inferior in the detection of superficial mucosal disease but reliably discloses the presence of severe inflammatory changes within the bowel wall and beyond, which may be underestimated from the endoscopic aspect of the mucosal surface. MRE helps to rule out severe stenoses that should be referred for immediate surgical intervention. In conclusion, both modalities are complementary and MRE should be used in more severe cases of Crohn's disease and in patients who might have involvement beyond the mucosa of the small bowel.