The present invention relates to the field of nutrition for children. In particular, the present invention relates to the nutritional compositions intended for children with an impaired function of the gastro-intestinal tract. One embodiment of the present invention relates to a nutritional composition to be administered to children with an impaired function of the gastrointestinal tract comprising probiotic micro-organisms. The probiotic micro-organisms may be non-replicating, for example bioactive heat treated probiotic micro-organisms.