The diagnosis and surgical treatments of Hirschsprung's disease (HD) have undergone various changes in the last few decades because of establishment of laparoscopic procedures. A retrospective nationwide survey for 4 decades was performed to study the changing profile of HD in Japan. The patient data were collected in 4 phases: Group 1, between 1978 and 1982; Group 2, between 1988 and 1992; Group 3, between 1998 and 2002; and Group 4, between 2008 and 2012. The incidence and the male/female ratio remained almost the same over time (1/4, 895 in newborns and 2.9:1 in Group 4). The patients with a family history increased to 7.1% in Group 4, in comparison to 2.8-6.0% in other groups. Regarding the extent of aganglionosis, sigmoid colon increased to 63.1% in Group 4, compared to 51.9% in Group 3. Manometry was performed less frequently in Group 4 (45.8%) than in Group 3 (66.1%). Transanal endorectal pull-through (TAEPT) was the most popular operation in Group 4 (49.6%). In addition, laparoscopy-assisted operations increased to 46.9% in Group 4, in comparison to 29.7% in Group 3. The incidence of preoperative enterocolitis and the mortality rate in Group 4 were 17.2% and 2.4%, respectively, and were markedly decreased in comparison to Group 1 (29.2% and 6.5%, respectively). The mortality rate decreased over time to 2.4% in Group 4. Over the last decade, there has been remarkable improvement in the mortality rate associated with the small intestine (aganglionosis extending orally to more than 30cm of the terminal ileum). The rates were 25.5% in Group 4, 53.6% in Group 1, 33.3% in Group 2, and 35.5% in Group 3. In addition, the mortality rates of the remaining aganglionosis subgroups also improved. Primary operations without laparotomy, including TAEPT and laparoscopy-assisted operations, have become the first choice for the definitive surgical treatment of HD in Japan. The mortality rate has decreased over time. However, the mortality rate of small intestinal aganglionosis is still relatively high. The development of new treatment strategy for small intestinal aganglionosis is called for.