Background: The heterogeneity of rectal biopsy techniques has encouraged us to search for a surgical and pathological standardisation of this diagnostic technique to exclude Hirschsprung’s disease. The different amounts of information on the anatomopathology report prompted us to compile a template for the anatomopathology report for diagnostic rectal biopsies for surgical colleagues and pathologists working on Hirschsprung’s disease. Methods: We gathered the anonymous biopsy information and its pathology information from five hospitals for all patients in which rectal biopsies were taken to diagnose Hirschsprung’s disease over two years (2020–2021). Results: Of the 82 biopsies, 20 suction (24.4%), 31 punch (37.8%) and 31 open biopsies (37.8%) were taken. Of all biopsies, 69 were conclusive (84.2%), 13 were not (15.8%). In the suction biopsy group, 60% were conclusive and 40% were not; for punch biopsy, the values were 87% and 13%, respectively and for open biopsy, 97% and 3%. Inconclusive results were due to insufficient submucosa in 6/8 suction biopsies, 4/4 punch biopsies and 0/1 open biopsies. An insufficient amount of submucosa was the reason for an inconclusive result in 6/20 cases (30%) after suction biopsy, 4/31 (12.9%) cases after punch biopsy and 0 cases (0%) after open biopsy. We had one case with major postoperative bleeding post suction biopsy; there were no further adverse effects after biopsy. Conclusions: Diagnostic rectal biopsies in children are safe. Non-surgical biopsies are more likely to give inconclusive results due to smaller amounts of submucosa present in the specimen. Open biopsies are especially useful when previous non-surgical biopsies are inconclusive. An experienced pathologist is a key factor for the result. The anatomopathology report should specify the different layers present in the specimen, the presence of ganglion cells and hypertrophic nerve fibres, their description and a conclusion.