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Eighty to ninety percent of Hirschsprung's disease (HD) patients present in newborns. However, the diagnosis of HD in the neonatal period remains difficult. Our present study aims to propose a diagnostic scoring system and hope this will increase early diagnosis of HD and avoid unnecessary rectal biopsy. Methods: In the first study period, 57 suspected HD patients (0-3 months) completed our predetermined study protocol in which barium enema (BE), rectal manometry (RM) and full-thickness rectal biopsy were performed. Symptoms, signs and investigations were analysed for their correlation with HD diagnosis. A HD diagnostic scoring system was developed according to the statistical results and was assessed in 74 patients in the second study period. Results: Forty-five patients were diagnosed with HD in the first study period. A HD scoring system was developed in which delayed meconium, tight anus, BE and RM were diagnostic factors. A cut-off point of 3 provided 84% of HD patients score > 3, whereas 75% non-HD patients score £ 3 (p < 0.05). In the second study group, patients with score £ 3 were selected for rectal biopsy. Conclusion: In the neonatal period, using a HD scoring system may help to select patients for further invasive investigation so that unnecessary biopsy can be avoided.