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Background This study aimed to assess the eosinophil (eos) density of the mucosa of the gastrointestinal (GI) tract in children undergoing endoscopic procedures following an extensive workup, without diagnosis of an organic disease. Methods Biopsies from GI endoscopies performed at 3 major children's hospitals (Athens, Madrid and Rome), between January 2012 and June 2018, were evaluated by a single pathologist in each center. Peak eos counts were expressed /high power field and /mm2. Other histological abnormalities were also reported. Results A total of 111 children (median age 11 years; 48 boys) underwent upper endoscopy (333 biopsies), while 44 (median age 12; 25 boys) underwent ileocolonoscopy (262 biopsies). The median (interquartile range) eos/mm2 were as follows: esophagus 0 (0-0); stomach 0 (0-3); duodenum 22 (13-29); ileum 29 (19-46); cecum 39 (25-71); ascending colon 24 (20-41); transverse colon 27 (21-57); descending colon 21 (13-27); sigmoid colon 22 (13-30); and rectum 10 (6-22). Geographical variations in GI tissue eos counts were found amongst the participating centers, but the causative factors need further evaluation. Functional GI disorders according to the Rome IV criteria were diagnosed in 73 children (37 boys, median age 13 years). No differences were found between children with or without functional GI disorder diagnosis, with regard to eos density in the GI tract. Conclusion The reported peak counts of GI tissue eos in children with no organic diseases provide normative values that may be useful in the evaluation of children with GI symptoms suggestive of eosinophilic GI disorders.