Ethanol-induced cell death has been characterized in very few stages of embryogenesis. This investigation comprehensively maps patterns of both programmed and ethanol-induced cell death in the central nervous system and craniofacial region at 0.5-day intervals from gestational day (GD) 6.5 to 11 in mice. A teratogenic dosage of ethanol (2.9 g/kg) or vehicle was administered via two intraperitoneal injections to pregnant C57BL/6J mice at various stages of gestation. Cell death patterns were characterized using Nile blue sulfate vital staining and histological analysis of plastic sections. Confocal laser scanning microscopy of LysoTracker Red-stained specimens allowed for three-dimensional visualization of areas of apoptosis and precise sectional imaging of mouse embryos. Apoptosis was also documented using a TUNEL technique on histological sections. Normal programmed cell death in control embryos was noted in the prechordal plate region at GD 8, the neuroepithelium of the fourth ventricle and anterior neuropore at GD 9, and within the ganglia of cranial nerves V, VII-VIII, IX, and X at GD 10. Acute maternal ethanol administration 12 hr before examination resulted in a dramatic increase in apoptosis within sites of programmed cell death in the embryo. Moreover, ethanol-exposed specimens exhibited stage-dependent excessive cell death in other distinct cell populations, particularly within the developing central nervous system. Ethanol-induced apoptosis was notable as follows: GD 7.5-neuroectoderm; GD 8-neural plate and primitive streak; GD 9-alar plate and presumptive neural crest of the rostral hindbrain, especially at the mesencephalon/rhombencephalon junction; GD 9.5-10-branchial arches and rhombomeres; and GD 11-diencephalon, basal ganglia, pons, and developing cerebellum. The results of this study revealed developmental stage-specific cell populations of the developing brain and craniofacial region that are vulnerable to ethanol-induced apoptosis and provide new insight relative to the genesis of alcohol-related birth defects.