A nationwide questionnaire survey of congenital hydrocephalus in 2000 investigated the treatment and clinical outcomes for congenital hydrocephalus in Japan to evaluate the factors influencing clinical outcome. Surgical treatment was performed in 341 of 380 patients who survived the early neonatal period. Of 321 patients who had shunt operations, 295 (91.9%) underwent ventriculoperitoneal shunting and nine (2.8%) ventriculoatrial shunting. Programmable valves were used in 83 (33.6%) of the 247 patients at the first shunting and in 97 (39.3%) at the last shunting. The incidence of complications after the first shunting was 55.4% (46 of 83 patients) in the programmable and 61.6% (101 of 164) in the non-programmable valve groups. The types of shunt complication differed significantly between these groups (p < 0.001), as the incidence of shunt infection and malfunction was lower in the programmable valve group. Clinical outcome was generally better with later delivery stage during gestation (p < 0.02). The clinical outcome was statistically significantly better in term patients who underwent early shunt placement than in those who underwent late shunt placement (p < 0.05).