Abstract Purpose Children with constipation and suspected Hirschsprung’s disease are referred for rectal biopsy. Since this is an invasive procedure, appropriate indications should be applied to minimize the number of “unnecessary” biopsies. Methods We reviewed all constipated children who underwent a rectal biopsy to diagnose a possible Hirschsprung’s disease at a tertiary referral hospital over a 6-year period (2013–2018). We registered clinical and demographic factors in these children and conducted correlation and multivariate regression analysis to evaluate the relation between these factors and a diagnosis of Hirschsprung’s disease. Results We identified 225 children, aged 0–17 years. In total, Hirschsprung’s disease was diagnosed in only 49/225 (22%). Among the 49 children with Hirschsprung’s disease, 29 (59%) were diagnosed in the neonatal period. Among girls, HD was confirmed in only 10/101 (10%) children, and only 1 of these 10 girls was older than 6 months at the time of the biopsy. The following factors correlated significantly with Hirschsprung’s disease diagnosis in children older than 1 month: “male sex”, “failure to thrive”, “gross abdominal distention plus vomiting” and “fulfils the Rome 4 criteria for functional constipation”. Conclusion In children referred for rectal biopsy, the factors most indicative of Hirschsprung’s disease were “male sex”, “failure to thrive”, “gross abdominal distention plus vomiting” and “fulfils the Rome 4 criteria for functional constipation”. Notably, the prevalence of Hirschsprung’s disease decreased with the increasing age of the children. Girls referred for a biopsy rarely had Hirschsprung’s disease, especially those older than 1 month.