Background and aims: Small bowel MR enteroclysis and wireless capsule endoscopy (WCE) are new diagnostic tools for the investigation of the small bowel. The aim of this study was to compare the diagnostic yield of WCE with MR enteroclysis in the detection of small bowel pathologies. Methods: A total of 36 patients were included in the study. Indications for imaging of the small bowel were proven or suspected small bowel Crohn's disease (CD; n=18), obscure gastrointestinal (GI) bleeding (n=14) and tumour surveillance (n=4). Results: In patients with Crohn's disease WCE detected significantly more inflammatory lesions in the first two segments of the small bowel compared with MR enteroclysis (12 patients vs. 1 patient, p=0.016). In 5 out of 14 (36%) patients with GI bleeding, angiodysplasia was detected as a possible bleeding source. Three of these patients had active bleeding sites detected by WCE. One patient had scattered inflammation of the mucosa. MR enteroclysis did not reveal any intestinal abnormalities in this patient group. MR enteroclysis provided extraintestinal pathologies in 10 out of 36 (28%) patients. Conclusion: In patients with Crohn's disease WCE revealed significantly more inflammatory lesions in the proximal and middle part of the small bowel in comparison to MR enteroclysis, whereas in patients with obscure GI bleeding WCE was superior to MR enteroclysis.