Aims: The present study compares preoperative magnetic resonance enterography (MRE) accuracy in diagnosing stenoses, abscesses and fistulas to intraoperative findings in Crohn's disease patients, and determines whether discordance between these methods alter surgical plans. Methods: Our study included 55 consecutive patients scheduled for elective surgery due to Crohn's disease in a single institution between January 2011 and May 2015, whose surgical findings were also compared to preoperative MREs. Data were retrospectively analyzed. Results: Among these 55 patients, we found 80 stenoses, 5 abscesses and 18 fistulas during surgery. The MRE sensitivity, specificity and accuracy, respectively, reached 100, 77.8 and 96.4% for stenoses; 80.0, 90.0 and 89.1% for abscesses; and 77.8, 83.8 and 81.8% for fistulas. The operative plan was modified for 7 patients (12.7%) due to erroneous MRE diagnoses. No patient needed conversion or an unplanned stoma placement due to an incorrect diagnosis using MRE. The MRE diagnosis did not agree with the surgical findings for 36 lesions, 16 of which resulted from adhesions that explained the incorrect MRE diagnoses. Conclusions: Hence, while MRE is a useful diagnostic tool preoperatively in Crohn's disease patients, the presence of intra-abdominal adhesions may cause erroneous diagnosis through MRE.