BACKGROUND Studies evaluating the correlation between endoscopic disease activity and noninvasive markers are scarce in inflammatory bowel disease (IBD). OBJECTIVE The aim of this study is to evaluate the accuracy of the fecal calprotectin (FC) assay as a marker of disease activity of IBD, as determined by an extensive endoscopic scoring system. METHODS Thirty-five children and adolescents with IBD [17 with ulcerative colitis (UC) and 18 with Crohn's disease (CD)] and 28 healthy volunteers were enrolled. FC levels were determined by ELISA. The sum of Matts' score for UC and the simple endoscopic score for Crohn's disease (SES-CD) were used. The ileal lesions were evaluated by ultrasonography. RESULTS In UC patients, there was a strong correlation between FC levels and the sum of Matts' score (r=0.838, p<0.01). FC levels were significantly elevated in endoscopically active patients (median 1,562.5 μg/g) as compared to patients in endoscopic remission (median 38.9 μg/g) or healthy controls (median 19.9 μg/g). In CD patients, there was a strong correlation between FC levels and the SES-CD score (r=0.760, p<0.01). The FC levels were significantly higher in endoscopically active patients (median 2,037.5 μg/g) than in endoscopically inactive patients (median 172.5 μg/g) or healthy controls (median 19.9 μg/g), respectively. The FC levels of patients with ileal wall thickening (median 2,225.0 μg/g) were significantly higher than healthy controls (median 19.9 μg/g) and patients lacking ileal wall thickening (median 17.5 μg/g), respectively. CONCLUSIONS The FC assay is a useful marker for the detection of mucosal inflammation in pediatric IBD patients.