Background Rectal biopsy for the diagnosis for Hirschsprung's disease (HD) can be performed in several ways. Suction rectal biopsy (SRB) is the most widely used method for neonates and younger infants while open strip biopsy (OSB) is reserved for older children. Current notions suggest that SRB should not be used in older infants due to perceived thicker fibrous tissue in their rectal walls leading to higher rates of inconclusive results. This study aims to compare the inconclusive rates of both methods in children of different age groups. Methods A retrospective study were carried out with patients aged 13 years who underwent SRB or OSB during a 4-year period in a single center. Rectal biopsies were performed on patients with HD with previous endorectal pull-through surgeries excluded. Primary outcomes were rates of inconclusive results for SRB and OSB overall and when divided into different age groups. Results 79 biopsies (57 SRB and 22 OSB) were included in the study. 12 biopsies (9 SRB and 3 OSB) were deemed inconclusive. There was no significant difference in the rate of inconclusive results between patients underwent SRB and OSB overall (15.8% vs 13.6%, p=1.000). The same results were obtained when patients were divided into under one year and over one year groups or other different age groups (30.0% vs 33.3%, p=1.000). Conclusions Despite low biopsy numbers, our study suggests that SRB provides comparable rates of inconclusive results with OSB in children of all age groups.