Background: : Hirschsprung's disease is a congenital disorder caused by the failure of neural crest cell migration, resulting in the absence of ganglion cells in the myenteric and submucosal plexuses. Histopathological examination with hematoxylin-eosin (H&E) staining is the gold standard, but its interpretation is often challenging. Immunohistochemical markers such as Calretinin and S100 have been developed to improve diagnostic accuracy.Objective: To compare the diagnostic value of Calretinin and S100 as immunohistochemical markers in establishing the diagnosis of Hirschsprung's disease. Methods: An observational analytical study with a cross-sectional design using 33 samples of patients with Hirschsprung’s disease who underwent biopsies at H. Adam Malik General Hospital, Medan, from 2022 to 2025. using McNemar’s exact test. Statistical significance was set at p < 0.05. The reference diagnosis was established based on histopathological evaluation of H&E staining in correlation with clinical findings and surgical outcomes, when available. Cases were classified as Hirschsprung’s disease if histological examination demonstrated the absence of ganglion cells, consistent with the clinical presentation of functional intestinal obstruction.Results: H&E + Calretinin examination showed positive results for Hirschsprung's disease in 81.8% of the cases, while H&E + S100 showed positive results in 78.8% of the cases (p = 0.002). The sensitivity and specificity of calretinin were 96.2% (95% CI: 81.0-99.9) and 83.3% (95% CI: 35.9-99.6) with an overall accuracy of 93.9%, whereas those of S100 were 96.1 % (95% CI: 75.7–99.1) and 71.4 % (95% CI: 35.9–99.6), respectively. with an overall accuracy of 90.9%. McNemar’s exact test revealed no statistically significant difference between Calretinin and S100 (p = 1.000)Conclusion: Calretinin has a higher diagnostic value than S100 in detecting Hirschsprung's disease, with better sensitivity and specificity. Although Calretinin showed slightly higher sensitivity, no statistically significant difference was observed between the two markers. Therefore, both markers may serve as reliable adjunct immunohistochemical tools to support the histopathological diagnosis of Hirschsprung’s disease.