Neural apoptosis in normal medaka (Oryzias latipes) embryos at stage 20 (the neural rod step in brain development), stage 27 (the neural tube step in brain development), and stage 29 (the late embryonic brain step in brain development) were examined, and the results were compared with those reported for other vertebrates, particularly zebrafish. Apoptotic cells were identified using TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling), by which fragmented DNA, which is characteristic of apoptotic cells, is labeled. Whole-mount TUNEL showed the following gross pattern of apoptotic changes during development. At stage 20, numerous single apoptotic cells were distributed diffusely in the entire regions of the brain. At stage 27, in addition to the diffusely distributed apoptotic cells, several large aggregates of TUNEL-positive structures (apoptotic centers) appeared in the brain and eyes. Histological observations of sections of the stained embryos revealed that apoptotic centers are present in the zona limitans intrathalamica, the ventral region of the optic stalk, several sites of the floor plate, and the retina. At stage 29, both single apoptotic cells and apoptotic centers decreased in number. This apoptotic pattern in medaka embryos is generally similar to that in zebrafish embryos, but apoptosis in the nervous system continues for a longer period in medaka than in zebrafish. Apoptosis in the vertebrate nervous system seems to be ubiquitous, random and probabilistic in nature.