In intestinal resection animal models of short bowel syndrome (SBS), the remaining epithelium mounts a robust adaptive response characterized by early stem cell expansion and increased crypt depth, villus height and nutrient absorption. In humans the adaptive response is critical for resumption of oral nutrition, yet it may be variable, and underlying mechanisms are much less well understood. Current knowledge relating to the role of stem and mesenchymal niche cells in the adaptive response in animal models and in human SBS are addressed in this review.