In the treatment of Hirschsprung's disease, transanal endorectal pull-through (TEPT) is being performed without laparoscopic assistance or laparotomy for short-segment aganglionosis. Preoperative ascertainment of the extent of aganglionosis is required, as this affects the planning for TEPT. The present study investigated the usefulness of preoperative endoscopic marking as an intraoperative marker of the location of pull-through. Since 1998, we have performed TEPT using a prolapsing technique for the treatment of Hirschsprung's disease. Subjects comprised 17 patients with short-segment aganglionosis and 2 patients with long-segment aganglionosis in whom endoscopic marking was performed preoperatively. Median age at time of surgery was 2.7 months. The relationship between pathologic findings at the marked area and location of actual pull-through was investigated. For endoscopic marking, each patient was sedated using intravenous ketamine hydrochloride. The junction between normal bowel with peristalsis and aganglionic bowel without peristalsis ("shorebreak" finding) was marked by either tattooing or clipping. Normal ganglion cells were seen in the marked area of 14 patients, and pull-through was performed at the marked area in each of these patients. In three patients, ganglion cells existed in the marked area, but the number of ganglion cells was considered insufficient. Additional frozen sections were thus prepared to ascertain the area with normal ganglion cells, showing that normal ganglion cells were seen 1, 3 or 5 cm proximal to the marked area. In one patient, no ganglion cells were seen in the marked area, but were present 5 cm proximal to the marked area. In the remaining one patient, normal ganglion cells were seen 7 cm distal to the marked area. Pathologic findings revealed ganglion cells at the shorebreak finding in 17 of the 19 patients (89.5%), suggesting that this junction basically matches the distribution of ganglion cells. Endoscopic marking of the junction is very useful for determining the tip of pull-through.