A nationwide survey in 2000 investigated the causative and associated central nervous system (CNS) lesions of congenital hydrocephalus in Japan. The etiology and associated diseases in 393 patients with congenital hydrocephalus were analyzed and compared between 193 patients with prenatally diagnosed (fetal) hydrocephalus and 181 with postnatally diagnosed (infantile) hydrocephalus. Of 393 patients of congenital hydrocephalus, 355 (90.3%) had primary hydrocephalus and 28 (7.1%) had secondary hydrocephalus. Of 355 patients with primary hydrocephalus, 85 (23.9%) had simple hydrocephalus associated with no other CNS anomaly and 270 (76.1%) had complicated hydrocephalus associated with other CNS anomalies. Destructive cystic lesions, holoprosencephaly, and agenesis of the corpus callosum were significantly predominant in fetal hydrocephalus. Arachnoid cyst was somewhat predominant in infantile hydrocephalus. The majority of cases of congenital hydrocephalus were primary hydrocephalus and two thirds were complicated hydrocephalus. Several complications showed marked predominance in fetal hydrocephalus.