A case is reported with aganglionosis of the rectum, sigma, and descending colon; dysganglionosis with heterotopic ganglionic cells in the muscularis propria of the hypoganglionic transverse colon; and extreme hypoganglionosis (without detection of ganglionic cells) of the ascending colon and distal ileum. The ileum showed a transition zone with hypoganglionosis and intestinal neuronal dysplasia (IND) type B. As to the etiology of such complex intestinal innervation defects, pre- and perinatal perfusion deficits must be considered because their localization seems to be linked to the vascular anatomy of the colon. Early diagnosis may be difficult, causing a delay in operative treatment and multiple operations. Different manifestations of dysganglionosis may be found in the same patient. The classical continuum of distal aganglionosis followed by proximal hypo- or dysganglionosis and then normally innervated bowel may not always be present. Therefore, in children with recurrent (sub-)ileus after resection of an aganglionic bowel segment, additional dysganglionosis such as IND or hypoganglionosis or even complex intestinal dysganglionosis should be excluded by full-thickness colon and small bowel biopsies.