Radiation-induced DNA damage introduces mutations that have various deleterious effects, which may lead to apoptosis and carcinogenesis. Different tissues and cell types exhibit varying degrees of sensitivity to radiation-induced DNA damage, which is often attributed to the frequency of cell division. In this study, we showed that irradiation affects early zebrafish embryos in a manner that is not explained by direct DNA damage and repair nor by the frequency of cell division. Zebrafish embryos irradiated at 2 h post fertilization showed drastic apoptosis, mainly in the head region, during organogenesis. Herein, we show that these apoptotic cells did not show aneuploidy or micronuclei, and that not all descendants of the same cells with the same DNA damage were necessarily apoptotic. Finally, we demonstrate that apoptotic cells have various origins and that neural crest cells have a sensitive cell fate. Our results suggest the existence of a radiation damage response mechanism other than those previously described, the elucidation of which may inform strategies for greater protection against radiation injury.