Experiments were designed to test the hypothesis that ethanol exposure during development can selectively affect the expression of specific isoforms of myelin protein gene expression in the rat cerebellum. We focused on myelin basic protein (MBP) and myelin-associated glycoprotein (MAG) gene expression. Both of these genes are alternatively spliced to yield 4 (MBP) or 2 (MAG) mRNA isoforms. Prenatal ethanol exposure, delivered to the dams in a liquid diet, did not significantly alter the expression of MBP or MAG gene expression in the cerebellums of 15-day-old pups, as measured by quantitative in situ hybridization using specific oligodeoxynucleotide probes. In contrast, postnatal ethanol exposure delivered directly to the pups over a 6-day period by gastrostomy tube (PN days 4-10) reduced the expression of specific MBP and MAG isoforms in the cerebellum of animals in adulthood. These data demonstrate that ethanol exposure, especially during the period of rapid myelination, has selective effects on mRNA isoforms encoding specific MBPs and MAG.