To prospectively compare the diagnostic accuracy of MR enteroclysis with duodenal intubation with MRI after drinking oral contrast agent only (MR enterography) with conventional enteroclysis (conv-E) as reference standard in patients with Crohn's disease. Forty consecutive patients (22 males and 18 females; mean age 36; range 16-74 years) with proven Crohn's disease underwent conv-E and MR imaging. Twenty-two patients underwent MR enteroclysis with intubation (MRE) and 18 underwent MR-enterography (MR per OS). Two radiologists reached a consensus about the following imaging findings: luminal distension and visualization of superficial mucosal, mural and mesenteric abnormalities. Standard descriptive statistics and a Wilcoxon rank sum test were used. Statistical significance was inferred at P < 0.05. There was no significant difference in the adequacy of luminal distention between the MRE and conv-E (P = 0.08), and both were statistically superior in comparison to MR per OS in the distension of the jejunum (P < 0.01) and less significant at the ileum and terminal ileum levels (P < 0.05). MRE and conv-E were comparable for the accuracy of superficial mucosal abnormalities; meanwhile conv-E compared with MR per OS was statistically superior (P < 0.01). MRE compared with MR per OS was statistically better when visualizing superficial abnormalities (P < 0.01). No statistically significant differences were found in assessing the diagnostic efficacy between MR examinations for the depiction of mural stenosis (P = 0.105) and fistulae (P = 0.67). The number of detected mesenteric findings was significantly higher with both MRE and MR per OS compared to conv-E (P < 0.01). MRE can serve as the diagnostic procedure for initially evaluating patients suspected of having Crohn's disease. MR per OS may have a role in patients that refuse or have failed intubation and also for follow-up.