Background & objectives: Hirschsprung’s disease is attributable to the congenital lack of ganglion cells in the far intestine. Rectal biopsy is deemed critical for its testing. In some instances, regular techniques fail to detect it. This study aims to evaluate the testing role of calretinin and CD56 immunohistochemistry and correlate the results to routine hematoxylin & eosin stained samples. Methods: This retrospective study was conducted in Rizgary Teaching Hospital, Erbil, Kurdistan region, Iraq. Rectal biopsies and colonic resection specimens of the clinically suspected Hirschsprung’s disease patients were collected and stained with calretinin and CD56 then their findings were compared to the hematoxylin and eosin stained sections during the period between February 2016 to October 2021. Results: Fifty patients aged from 3 days to 8 years with a male-to-female ratio of 3.6:1 were examined for rectal and colonic biopsies. Forty out of 50 cases were detected as HD by H&E staining. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy rate of calretinin were coherent with that of H&E-stained samples (100%), the likelihood ratio was 50 and the kappa test was 1, were superior to CD56 results with sensitivity (100%), specificity (90%), positive predictive value (97.5%), negative predictive value (100%), accuracy rate (98%), likelihood ratio was 27.77 and kappa test was 0.805. Conclusions: Immunohistochemical expression of calretinin is more specific and accurate than CD56 in HD diagnosis. Calretinin is a trustworthy, additional diagnostic tool for better morphological evaluation of ganglion cells and thereby assists in making a reliable diagnosis of HD.