Rectal suction biopsy (RSB) is the gold standard diagnostic procedure for disorders of bowel motility. This study describes our experience with RSB stained with histochemistry as the first diagnostic approach in a large series of patients presenting with chronic constipation. Between 1993 and 2005, 766 children underwent RSB for persistent chronic constipation. The specimens were snap frozen, sectioned and stained with conventional hematoxylin and eosin (H&E) and with nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) and acetylcholinesterase (AChE) histochemical stainings. Adequate amount of submucosa was present in 655 (85.5%) out of 766 cases and formed the basis of this study. RSB in 540 (82%) patients were reported as normal. Hirschsprung’s disease was found in 47 (7.2%) patients with characteristic features of absence of ganglion cells, increased AChE activity in the lamina propria and muscularis mucosae, thick nerve fibers in the submucosa, and a lack of NADPH-d-positive fibers in muscularis mucosae. RSB in 59 (9%) patients presented features of intestinal neuronal dysplasia such as submucosal hyperganglionosis, giant ganglia, ectopic ganglia and increased AChE activity in lamina propria. Hypoganglionosis was suspected in nine (1.3%) children because of sparse or absent ganglion cells and low AChE and NAPDH-d activity in muscularis mucosae. Three patients (0.4%) developed bleeding following RSB, requiring diathermy of the bleeding point. Thus, we conclude that RSB is a simple and safe method when used as the first diagnostic approach in patients with chronic constipation. The combination of two histochemical stainings techniques provides a high level of accuracy in the diagnosis of intestinal dysganglionosis.