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Background There is emerging evidence to suggest that Crohn’s disease (CD) may be a disease of the mesentery, rather than of the bowel alone. A more extensive mesenteric resection, removing an increased volume of mesentery and lymph nodes to prevent recurrence of CD, may improve clinical outcomes. This study aims to analyse whether more extensive ‘oncological’ mesenteric resection reduces the recurrence rate of CD. Methods This is an international multicentre randomized controlled study, allocating patients to either group 1—mesenteric sparing ileocolic resection (ICR), the current standard procedure for CD, or group 2—extensive mesenteric ICR, up to the level of the ileocolic trunk. To detect a clinically relevant difference of 25 per cent in endoscopic recurrence at 6 months, a total of 138 patients is required (including 10 per cent dropout). Patients aged over 16 with CD undergoing primary ICR are eligible. Primary outcome is 6-month postoperative endoscopic recurrence rate (modified Rutgeerts score of greater than or equal to i2b). Secondary outcomes are postoperative morbidity, clinical recurrence, quality of life, and the need for (re)starting immunosuppressive medication. For long-term results, patients will be followed up for up to 5 years to determine the reoperation rate for recurrence of disease at the anastomotic site. Conclusion Analysing these two treatment strategies in a head-to-head comparison will allow an objective evaluation of the clinical relevance of extensive mesenteric resection in CD. If a clinical benefit can be demonstrated, this could result in changes to guidelines which currently recommend close bowel resection. Registration number NCT00287612 (http://www.clinicaltrials.gov)