Diagnostic tools for paediatric chronic constipation have been limited, leading to over 90% of patients with treatment-resistant constipation being diagnosed with chronic idiopathic constipation, with no discernible organic cause. Work in our institution suggests that a number of children with intractable symptoms actually have slow colonic transit leading to slow transit constipation. This paper reviews recent data suggesting that a significant number of the children with chronic treatment-resistant constipation may have organic causes (slow colonic transit and outlet obstruction) and suggests new approaches to the management of children with chronic treatment-resistant constipation.