Severe chronic diarrhoea secondary to enterocolitis is a severe complication of Hirschsprung's disease (HSCR). Persistent outlet obstruction, immunologic issues, and mucin/mucous imbalance can cooperate in the development of this complication. Furthermore, isolated reports described severe postoperative chronic diarrhoea mimicking enterocolitis in patients with sucrase-isomaltase deficiency, inflammatory bowel disease (IBD), or intestinal microvillus atrophy. This paper is aimed in describing three patients from our HSCR series who experienced severe chronic postoperative diarrhoea secondary to such uncommon associated anomalies: sucrase-isomaltase deficiency (one patient) and IBD (two patients). With an appropriate sucrose-free diet or immunosuppressive therapy these patients improved dramatically and their diarrhoea settled. These associated anomalies can be diagnosed with digestive endoscopies (both gastro-duodenoscopy and colonoscopy). Therefore, we developed a diagnostic and therapeutic algorithm for patients with chronic diarrhoea after a pull-through, which includes digestive endoscopy to be performed in selected cases.