A number of pharmacologically and electrophysiologically distinct voltage-dependent Ca2+ channels have been identified in mammalian neurons. Two rat brain Ca2+ channel alpha 1 subunits (rbC-I and rbC-II) have been isolated by molecular cloning and shown to be highly related (95%) to the cardiac dihydropyridine-sensitive Ca2+ channel. The rbC-II protein is distinct from rbC-I in that it contains a 3 amino acid insert in the putative cytoplasmic loop between domains II and III and a 28 amino acid substitution corresponding to the third transmembrane segment (S3) of the fourth domain. We show that rbC-I and rbC-II transcripts are generated by alternative splicing and that they are differentially expressed in the rat CNS.