Laparoscopic Roux-en-Y gastric bypass (RYGB) is considered the 'gold standard' for surgical treatment of morbid obesity. It is hypothesised that reducing the length of the common limb positively affects the magnitude and preservation of weight loss but may also impose a risk of malnutrition. The aim of this study was to compare patients' nutrient and vitamin deficiencies in standard RYGB with a very long Roux limb RYGB (VLRL-RYGB). This study was part of the multicentre randomised controlled trial (Dutch Common Channel Trial), including 444 patients undergoing an RYGB or a VLRL-RYGB. Laboratory results, use of multivitamin supplements and reoperations were collected at baseline and 1 year postoperative. Primary outcome measure was nutrient deficiency after 1 year postoperative. Secondary outcome measure was the reoperation rate due to malabsorption. In total, 227 patients underwent RYGB and 196 patients underwent VLRL-RYGB. Most common deficiencies at 1 year postoperative were ferritin (17·2-18·2 %), Fe (23·4-35·6 %), K (7·4-15·2 %), vitamin B12 (9·0-9·9 %) and vitamin D (22·7-34·5 %). Patients undergoing VLRL-RYGB had slightly but significantly lower levels of Ca, Fe and vitamin D compared with those undergoing RYGB at 1 year postoperative, but significantly higher levels of folic acid and Na. Reoperation rates due to malabsorption were not significantly different between RYGB (2/227, 0·9 %) and VLRL-RYGB (7/196, 3·6 %) (P = 0·088). We concluded that patients undergoing VLRL-RYGB had significantly lower levels of Ca, Fe and vitamin D compared with those undergoing RYGB at 1 year postoperative, but higher levels of folic acid and Na. Reoperation rates did not differ. Close monitoring on nutrient deficiencies should be performed in patients undergoing VLRL-RYGB.