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Calprotectin is an abundant neutrophil protein that is extremely stable in feces. The aim of this study was to assess the effectiveness of fecal calprotectin as a noninvasive measure of disease activity in childhood inflammatory bowel disease (IBD) by comparison to a modified Lloyd-Still and Green score and laboratory inflammatory indices.Spot fecal samples from 37 children with IBD and 31 control children were sent by ordinary mail to the laboratory. Fecal calprotectin concentration was measured by an in-house enzyme linked immunosorbent assay (ELISA). A modified Lloyd-Still & Green score (mLSS) was calculated for each child with IBD within 10 days of obtaining the fecal sample.Compared with control values (median, range) (2.1, 0.5–6.3 mg/L), fecal calprotectin was increased in 16 children with ulcerative colitis, (11.5, 0.6–272.5 mg/L, P < 0.001) and in 21 children with Crohn disease, (14.0, 0.7–59.7 mg/L, P < 0.001). Twelve “moderately affected” children (mLSS of 35–65) had higher fecal calprotectin concentrations (22.2, 2.7–141.7 mg/L) than 25 “mildly affected” children (mLSS > 65), (10.3, 0.6–272.5 mg/L, P = 0.002). For the total IBD group, fecal calprotectin concentration correlated negatively with the mLSS (r = - 0.61, P < 0.001). It also correlated negatively with serum albumin concentration (r = - 0.49, P = 0.002) and positively with erythrocyte sedimentation rate (r = 0.40, P = 0.01).Fecal calprotectin seems to reflect bowel inflammation in children with IBD. As a simple, safe, noninvasive test, it has the potential to reduce the number of invasive investigations performed in these children.