Neural stem cells (NSCs) can be differentiated into one of three cell lineages: neurons, astrocytes or, oligodendrocytes. Some neurotoxins have the ability to deregulate this dynamic process. NSC cell fate can be altered by ethanol as reported previously. Our aim was to investigate the alteration of genes by ethanol during NSC differentiation and to explore the molecular mechanism underlying this phenomenon. Here, mouse fetal forebrain derived NSCs were differentiated for 2 days with or without of ethanol (50 mM). We performed a comparative microarray analysis at day two using GeneChip(®) Mouse Genome 430A 2.0 arrays. Microarray analysis showed that the expressions of 496 genes were altered by ethanol (56 and 440 were up- and down-regulated, respectively). Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed the association of the following altered genes in the Wnt signaling pathway: Wnt5a, Csnk2a1, Tcf7l2, Ccnd2, Nlk, Tbl1x, Tbl1xr1, Rac2 and Nfatc3. Quantitative real time PCR analysis also demonstrated the relative expression levels of these genes. As Wnt signaling is a player of brain development, ethanol-induced alterations may contribute to improper development of the brain. Our data could be a useful resource for elucidating the mechanism behind the ethanol neurotoxicity in developing brain.