The alpha 1E voltage-dependent calcium channel has not been clearly identified with a specific neuronal calcium current. To help identify the role of alpha 1E, we examined differential expression of alpha 1E splice variants in mouse brain and cultured cell lines and examined the gene structure of the region encoding the amino terminal. Three splice variants were analyzed by a ribonuclease protection assay, and a fourth variant reported previously in a fetal human alpha 1E sequence was also detected in mouse brain and a pituitary cell line. Whole brain, telencephalon, and olfactory bulb contained predominantly the splice variant corresponding to alpha 1E-1 although other known variants could be detected. Neuroendocrine cells in vitro (beta TC3 insulinoma cells and AtT-20 pituitary cell lines) expressed predominantly one alpha 1E isoform. The existence of a 5' exon accounting for the origin of variant 5' ends reported in different species was suggested by the sequence of the mouse alpha 1E gene in the region encoding the amino terminal.