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Background Internal herniation is a well known and potentially life-threatening complication of laparoscopic Roux-en-Y gastric bypass (LRYGB). The aim of this study was to evaluate the benefit and harm of closing the mesenteric defects with clips during LRYGB to prevent internal herniation. Methods This was a single-centre, single-blinded RCT. Patients eligible for LRYGB were randomized to surgery with or without closure of mesenteric defects with clips. The primary endpoint was the incidence of (intermittent) internal herniation after LRYGB with a minimum follow-up of 24 months. Secondary outcomes were duration of surgery, number of clips used, trocars and sutures used, postoperative pain measured by a visual analogue scale (VAS), and postoperative complications. Results Between 13 August 2012 and 18 May 2017, 401 patients were randomized to closure (201) or non-closure (200) of mesenteric defects. Median follow-up for both groups was 59 months (range 8–67 and 16–67 months in non-closure and closure groups respectively). The cumulated risk of internal herniation after 2 years was 8.0 per cent in the non-closure group compared with 4.5 per cent in the closure group (hazard ratio (HR) 1.81, 95 per cent c.i. 0.80 to 4.12; P = 0.231). At 5 years, rates were 15.5 and 6.5 per cent respectively (HR 2.52, 1.32 to 4.81; P = 0.005). Closure of mesenteric defects increased operating time by a median of 4 min (95 per cent c.i. 52 to 56 min for the non-closure group and 56 to 60 min for the closure group; P = 0.002). There was no difference in postoperative blood transfusion rates and VAS scores between the groups. Conclusion Routine closure of the mesenteric defects in LRYGB with clips is associated with a lower rate of internal herniation. Registration number: NCT01595230 (http://www.clinicaltrials.gov).