Rectal suction biopsy is the diagnostic procedure of choice in aganglionosis even if only mucosal tissue is obtained. In neuronal intestinal dysplasia it is essential to include parts of the submucous layer. Therefore some biopsies are unsuitable because they lack submucous tissue. In a retrospective analysis (1991-1993) this occurred in 34.9% of our biopsies. These samples were taken without attention to the level of suction. Prospectively we compared suction biopsies taken by a standard suction level (250-300 cm water column) with excision biopsies taken by scissors under speculum exposure in ten consecutive patients. Submucosa was missed in only one biopsy each, but two excision biopsies were made useless by mechanical traumatization. We conclude a correctly practised rectal suction biopsy still remains the procedure of choice for diagnostic screening in malformations of the enteric nervous system.