Background <p>Defecation dysfunction among patients with Hirschsprung disease (HD) in early childhood may persist into adulthood and lead to social problems. The features of defecation dysfunction in HD patients with different aganglionic segment lengths during early childhood have not been established. The present study was designed to identify and describe the features of defecation dysfunction among patients with HD in early childhood.</p> Methods <p>Two hundred four children with HD and 156 healthy children (control group) were asked to complete a questionnaire (bowel function score [BFS]) to evaluate defecation status. The HD patients were divided into three groups: rectosigmoid HD (RSHD), in which the aganglionic segment was restricted to the rectosigmoid (<i>n</i> = 148); descending or transverse HD (DTHD), in which the aganglionic segment extended to the descending or transverse colon (<i>n</i> = 39); and ascending colon or ileum HD (AIHD), in which the aganglionic segment extended to the ascending colon or terminal ileum (<i>n</i> = 17). The results of the BFS were compared among the RSHD, DTHD, AIHD, and healthy control groups.</p> Results <p>The defecation dysfunction rates in the RSHD, DTHD, and AIHD groups were 27.7%, 71.8%, and 100%, respectively, and were significantly higher than the healthy control group rate (all <i>P</i> &lt; 0.05). No apparent correlation was detected between age and the total BFS at the follow-up evaluation in the RSHD and DTHD groups (Spearman’s rank correlation coefficient: ρ = 0.081, <i>P</i> = 0.329 and ρ = 0.081, <i>P</i> = 0.626, respectively). With the exception of constipation, the prevalence of normal bowel function items, such as the ability to delay defecation, feeling the urge to defecate, reporting the urge to defecate, the frequency of defecation, soiling, accidents, and social problems, was significantly lower in the RSHD, DTHD, and AIHD groups than the healthy control group (all <i>P</i> &lt; 0.05) and exacerbated as the length of the aganglionic segment increased (all <i>P</i> &lt; 0.05).</p> Conclusion <p>Defecation dysfunction was shown to be prevalent in all HD anatomic types during early childhood and gradually became more severe as the length of the aganglionic segment increased but did not improve with age. The defecation dysfunction features were characterized by an inadequate ability to delay defecation, feeling the urge to defecate, reporting the urge to defecate, frequent bowel movements, soiling, accidents, and social problems, which also worsened as the aganglionic segment increased in length. Constipation was not prevalent and was not a major issue among HD patients in early childhood.</p> Trial registration <p>This study was registered at ClinicalTrails.gov on 30/11/2022 (NCT05655845).</p>