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In young children, the use of fecal calprotectin (fCP) as a biomarker is limited because reference values have not been widely accepted up to now. Moreover, reference values for fecal eosinophil–derived neurotoxin (fEDN) in children have not been established. The aim of the present study was to investigate fCP and fEDN levels in young healthy children to establish reference values.Stool samples were obtained from healthy children ages 0 to 12 years. fCP and fEDN levels were analyzed using the EliA Calprotectin 2 assay (Phadia AB) and a novel research assay (on the ImmunoCAP platform), respectively.In the 174 included children (87 boys), 95th Percentile values ranged from 1519 mg/kg at 0 months to 54.4 mg/kg at 144 months for fCP and from 9.9 mg/kg at 0 months to 0.2 mg/kg at 144 months for fEDN. There was a statistically significant association between age and fCP concentrations (P < 0.001) and age and fEDN concentrations (P < 0.001). We also found a statistically significant association between fEDN and fCP concentrations (rho = 0.52, P < 0.001). According to our results, we provide a nomogram and we suggest 3 different age groups for evaluation of fCP and fEDN concentrations, the 95th percentile being respectively 910.3 and 7.4 mg/kg for 0–12 months, 285.9 and 2.9 mg/kg for >1 to 4 years, and 54.4 and 0.2 mg/kg for >4 to 12 years.By using an improved analytical method, we have confirmed that young healthy children have higher fCP concentrations than healthy adults. We, for the first time, report reference values for fEDN concentrations in a pediatric population. The proposed nomograms and reference values for fCP and fEDN are aimed at facilitating the applicability of biomarkers for both neutrophil- and eosinophil-mediated intestinal inflammation in children in clinical practice.