Reported incidence of small bowel obstruction (SBO) after laparoscopic Roux-en-Y gastric bypass varies between 1.5% and 3.5%. It has been suggested that the antecolic antegastric laparoscopic Roux-en-Y gastric bypass (AA-LRYGB) is associated with a low incidence of internal herniation (IH). Therefore we routinely did not close mesenteric defects. The records of 652 consecutive patients undergoing primary AA-LRYGB from January 2003 to December 2009 in a single institution were retrospectively reviewed to determine the incidence, etiology, clinical symptoms, radiologic diagnostic accuracy and operative outcomes of SBO. Of the 652 patients, 63 (9.6%) developed SBO. The majority (6.9%, 45 patients) had a SBO due to IH. In 41 (91%) cases, the IH was at the jejunojejunostomy (JJ), four cases had an IH at Petersen's space. Adhesions and ventral hernia were found in 14 (2.1%) and four (0.6%) cases, respectively. Twenty-nine out of 63 cases had negative computed tomography (CT) findings and IH was diagnosed on CT in only 33% (14/45) of patients with IH. All patients underwent diagnostic laparoscopy. No bowel resections had to be performed. In contrast to previous reports, a high incidence of SBO with a high rate of IH at the JJ site was found in our series. Accuracy of CT is low and diagnostic laparoscopy is mandatory when SBO is suspected. Since 2010 we have started closing the JJ site, and data on SBO are collected prospectively. We believe that closing of the mesenteric defects is a mandatory step, even in an AA-LRYGB.