AIM: To compare the results of high-resolution ultrasound (HR-US) and magnetic resonance enterography (MRE) examinations in patients with inflammatory bowel disease (IBD). METHODS: The reports of 250 consecutive cases with known IBD, who had an MRE and HR-US examination, were retrospectively analyzed. Using a patient-based approach we evaluated morphological disease features such as affected bowel wall, stenosis, abscess and fistula. The comparison between the two modalities was based on the hypothesis, that any pathological change described in any imaging modality was a true finding, as no further standard of reference was available for complete assessment. RESULTS: Two hundred and fifty examinations representing 207 different patients were evaluated. Both modalities assessed similar bowel wall changes in 65% of the examinations, with more US findings in 11% and more MRE findings in 15%. When the reports were analyzed with regard to "bowel wall inflammation", US reported more findings in 2%, while MRE reported more findings in 53%. Stenoses were assessed to be identical in 8%, while US found more in 3% and MRE in 29% (P < 0.01). For abscess detection, US showed more findings in 2% (n = 4) while MRE detected more in 6% (n = 16). US detected more fistulas in 1% (n = 2), while MRE detected more in 13% (n = 32) (P < 0.001). The most common reason for no detected pathology by US was a difficult to assess anatomical region (lesser pelvis, n = 72). CONCLUSION: US can miss clinically relevant pathological changes in patients with IBD mostly due to difficulty in assessing certain anatomical regions. (C) 2011 Baishideng. All rights reserved.