Calprotectin is a calcium- and zinc-binding protein of the S100 family expressed mainly by neutrophils with important extracellular activity. This paper reviews current findings concerning the relationship between faecal calprotectin and intestinal development among children, influencing factors of fecal calprotectin and the implication of faecal calprotectin in the diagnosis, follow-up, assessment of relapses, and response to treatment in pediatric intestinal diseases, such as necrotizing enterocolitis, inflammatory bowel disease, intestinal infection, celiac disease and allergy. Further studies are required to provide insights into the actual role of calprotectin in physiological and pathological processes in pediatrics.