The invention relates to systems or kits and methods for repairing defects in gastric bypass operations, e.g., methods of closing intragastric fistulas (18, 20) and dilated gastrojejunal anastomoses. In various embodiments, an endoscopic suturing device (23) is inserted through a patients mouth, down through the esophagus, and positioned in the region of the defect, e.g., fistula. Adjacent tissue is then acquired, e.g., by vacuum, and one or more stitches are placed through the tissue and tightened to at least partially close the fistula, forming a suture line. One or more reinforcing clips (30) and sealant (32) can be endoscopically applied to the suture line.
