Side-to-side, functional end-to-end stapled anastomosis (SS-EESA) is a frequently employed technique to re-establish continuity following bowel resection. We describe, for the first time in children, two cases of an important complication of this form of bowel anastomosis. Patient 1 had resection of a jejunal lymphangioma and formation of an SS-EESA at the age of 3 years. By the age of 7 years he was demonstrating symptoms consistent with malabsorption, which was confirmed by hydrogen breath testing. An upper GI contrast study indicated a segmental dilatation of the distal small bowel. Elective laparotomy revealed partial volvulus of a greatly dilated SS-EESA. Patient 2 had undergone bowel resection as a neonate for ileal atresia, with end-to-end anastomosis. An anastomotic stricture developed at two months of age that was resected with formation of an SS-EESA. Multiple ensuing episodes of partial small bowel obstruction were managed non-operatively until, at 5 years of age, she presented with complete bowel obstruction. At operation, volvulus of a hugely dilated SS-EESA was found. Intraoperative cultures of the succus entericus were consistent with bacterial overgrowth. Both patients were successfully treated with resection of the SS-EESA and primary anastomosis. SS-EESA can be complicated by bacterial overgrowth, massive dilatation and volvulus. In patients with SS-EESA who present with recurrent obstructive symptoms, this complication should be considered.