The sensitivity of the developing central nervous system (CNS) to the deleterious effects of ethanol has been well documented, with exposure leading to a wide array of CNS abnormalities. Certain CNS regions are susceptible to ethanol during well-defined critical periods. In the neonatal rodent cerebellum, a profound loss of Purkinje cells is found when ethanol is administered early in the postnatal period [on postnatal days 4 or 5 (P4-5)], while this neuronal population is much less vulnerable to similar ethanol insult slightly later in the postnatal period (P7-9). Prior studies have shown that neurotrophic factors (NTFs) can be altered by ethanol exposure, and both in vitro and in vivo studies have provided evidence that such substances have the potential to protect against ethanol neurotoxicity. In the present study, it was hypothesized that depletion of an NTF shown to be important to cerebellar development would exacerbate ethanol-related effects within this region, when administration was confined to a normally ethanol-resistant ontogenetic period. For this study, brain-derived neurotrophic factor (BDNF) gene-deleted ("knockout") and wild-type mice were exposed to ethanol via vapor inhalation or to control conditions during the normally ethanol-resistant period (P7 and P8). Two hours after termination of exposure on P8, analyses were made of body weight, crown-rump length, and brain weight. In subsequent investigations, the number and density of Purkinje cells and the volume of cerebellar lobule I were determined, and the expression of anti- and pro-apoptotic proteins and the activities of endogenous antioxidants were assessed. It was found that the BDNF knockouts were significantly smaller than the wild-type animals, with smaller brain weights. Purkinje cell number and density was reduced in ethanol-treated knockout, but not wild-type animals, and the volume of lobule I was significantly decreased in the gene-deleted animals compared to wild-types, but was not further affected by ethanol treatment. The loss of Purkinje cells in the BDNF knockouts was accompanied by decreases in anti-apoptotic Bcl-xl and in phosphorylated (and hence inactivated) pro-apoptotic Bad, and reduced activity of the antioxidant glutathione reductase, while the antioxidant catalase was increased by ethanol treatment in this genotype. In the wild-type animals, anti-apoptotic Bcl-2 was decreased by ethanol treatment, but the pro-apoptotic c-Jun N-terminal kinase (JNK) was markedly diminished by ethanol exposure, while the activity of the protective antioxidant superoxide dismutase (SOD) was significantly enhanced. These results suggest that neurotrophic factors have the capacity to protect against ethanol neurotoxicity, perhaps by regulation of expression of molecules critical to neuronal survival such as elements of the apoptosis cascade and protective antioxidants.