Aims: Faecal calprotectin, a neutrophil cytosolic protein, is raised in inflammatory bowel disease. We assessed this investigation in evaluating children with chronic intestinal symptoms. Methods: Stool samples from 100 children aged 5-17 years (referrals to the regional paediatric gastroenterology service) were tested using a commercially available kit. Results: Calprotectin was higher in inflammatory bowel disease than normal children (p < 0.0001) or in those with functional constipation (p < 0.0001). The overall specificity for organic bowel disorders was 85%. Calprotectin correlated with C-reactive protein in inflammatory bowel disease (p = 0.001), and clinical disease activity in ulcerative colitis (p = 0.017), but not with disease activity in Crohn's disease. Conclusion: Raised faecal calprotectin should prompt further assessment in children with chronic intestinal symptoms, since an organic bowel disorder is likely. However, calprotectin cannot be regarded as a specific test for idiopathic inflammatory bowel disease.