Jejunojejunal intussusception occurred after jejunal resection and stapled functional end-to-end anastomosis in two pony mares. In both mares, the lead point of the intussusception was the stapled functional end-to-end (FEE) anastomosis. The stapled free ends of jejunum were oversewn with an inverting suture pattern. A possible explanation for development of the intussusception was the acute angle created in the intestine by the FEE anastomsis. This angulation may have impaired flow of ingesta causing motility changes that predisposed the site to intussusception. Because the oversewn blind intestinal ends acted as the lead point for formation of the intussusception, it may be inadvisable to oversew the stapled anastomotic ends.