Background Hirschsprung’s disease (HD) is due to malfunction of neural crest cell migration to the distal bowel, resulting in colonic aganglionosis. Hypoganglionosis and intestinal neuronal dysplasia (IND) are other neuronal causes of paediatric intestinal obstruction. These two entities have been reported to occur concurrently with HD. Their occurrence in the Malaysian HD population remains unknown. This knowledge is important to avoid the diagnostic pitfalls of transition zone evaluation, especially in intraoperative frozen section procedure. Aim To investigate the prevalence of hypoganglionosis and IND in resected bowel specimens for HD. Methods Thirty-nine resected bowel specimens from HD cases were retrieved from the archives of Pathology Department, Hospital Kuala Lumpur. The H&E stained sections from these cases were reviewed for the neuronal abnormalities stated above. Results Demographically, 79.4% of the patients were male. The age at operation ranged from 11 weeks to 4.9 years. Culturally, 66% were Malays, 17% Chinese, 12.8% indigenous Borneo ethnic group and 2.5% Indian. All of the cases had recto-sigmoid disease. Giant ganglia and hypoganglionosis were seen in 7 (17%) and 4 (10.3%) cases, respectively. In addition, an excess of small ganglions were present within the transtition zone of 24 cases (61.5%), while ectopic ganglia were observed in 2 cases. Conclusion IND is not uncommon in HD patients in Malaysia. This is important to appreciate, especially in the assessment of resection margins of HD.