A detailed histological examination of mast cells (MC) distribution from the oesophagus to the rectum in healthy patients and those with gastrointestinal food allergies (GFA) was done to determine a physiological and illness-defining cut-off. The reference cohort consisted of 9 children individuals who had regular histological examinations or undergone endoscopy for surveillance purposes after a previous polypectomy for single colonic juvenile polyps. A chronic inflammatory condition (e.g., inflammatory bowel disease, celiac disease) or allergy was ruled out in all these people. In addition, a group of 15 individuals with gastrointestinal issues that were thought to be caused by a GFA were also studied. CD117 (c-Kit) was used as a valid marker to detect MCs in the lamina propria in immunohistochemistry from all samples. There were significant disparities in MC numbers in all sections of the paediatric gastrointestinal (GI) tract. The duodenum, terminal ileum, cecum, and ascending colon had the most significant MC levels in both symptomatic and control subjects. In the oesophagus, the lowest numbers were recorded. The gastric corpus (22.1±4.0/high power field [HPF] vs 32.0±10.1/HPF; P=0.034) and ascending colon (44.8±10.4/HPF vs 60.4±24.3/HPF; P=0.047) showed significant differences between GFA and healthy participants. The number of mucosal MC cells in the pediatric GI tract was higher than previously thought, with much overlap between healthy and GFA patients. The outcomes provide precise information on the location and quantity of MCs in pediatric allergy patients and, for the first time, estimates for physiological values in children. Additional laboratory parameters must be added to GFA diagnostic processes.