Maternal intraperitoneal administration of 1 mg/kg 5-azacytidine to pregnant S1c:ICR mice on gestational Day 7.5 resulted in a high incidence of exencephalic offspring. Histological examination of untreated 7.5 days mouse embryos revealed that the head folds were formed in the anterior halves of the embryos, whereas the primitive streaks still remained in the posterior halves. At 12 hours after 5-azacytidine administration (8.0 days embryos), numerous pyknotic cells were observed in the neurectoderm of the head folds, in the embryonic ectoderm and the migrating mesoderm of the primitive streak region. These pyknotic cells had almost disappeared from the embryonic tissues, and few abnormalities were encountered, in embryos 24 hours after 5-azacytidine administration (8.5 days embryos), except for the slight reduction in thickness of the neurectoderm of the head folds compared with that in untreated 8.5 days embryos. In untreated 9.5 days embryos, the head folds had entirely closed along the anterior neuroaxes, whereas those treated with 5-azacytidine 48 hours earlier displayed head folds that were open in various degrees along the neuroaxes anterior to the fourth ventricle. The primary cause of 5-azacytidine-induced exencephaly is considered to be attributable to a powerful cell-killing action of 5-azacytidine and the subsequent loss of germinal cells in the neurectoderm of the head folds. The precise mechanisms by which this damage results in the failure of neural tube closure in the cephalic region remains unclear.