Extensive loss of small bowel in all age groups has significant morbidity and mortality consequences. Despite the astonishing ability of the small bowel to compensate for an extensive loss, long-term parenteral nutrition and enteral nutrition, tailored to the need of the patients in relation to the missing intestinal regions is needed. Organ-preserving surgical intervention becomes necessary in patients with a very short intestinal transit time and in an other group of patients with impaired propulsive peristalsis. Intestinal transplantation is indicated in recurrent septical infections or if nearly all of the small bowel is missing. This review discusses indications and risks of the organ-preserving surgical therapies in children with short bowel syndrome.