Objective: Hirschsprung’s disease may be associated with a number of congenital anomalies of which Down’s syndrome and intestinal atresias are commonly encountered. The study aimed to assess the impact of rare associated anomalies on the diagnosis and management of Hirschsprung’s disease.Methods: A retrospective review of the clinical presentation, diagnosis and outcome of thirty five consecutive newly diagnosed cases of Hirschsprung’s disease encountered over two years was performed.Results: Besides Down’s syndrome (two), intestinal atresia (one) and pigmentary ocular defects (two), three rare anomalies (Occipital meningocele, Calcific meconium cyst with anal stenosis, Malrotation) were encountered in four of thirty five cases. The clinical features, radiologic anatomy and gross morphology of the bowel were unconventional and the diagnosis was supported by intraoperative acetylcholinesterase staining of biopsies. Though the diagnosis was relatively delayed in these cases, the outcome has been comparable to the rest. The dilemma in their diagnosis and management and their possible pathoembryology is discussed.Conclusion: Awareness of such associations and a specific investigative protocol is imperative for timely diagnosis and minimal morbidity in complex presentations of Hirschsprung’s disease.