Carnitine palmitoyltransferase I (CPT-I) catalyzes the rate-determining step in mitochondrial fatty acid beta-oxidation. The enzyme has two cognate structural genes (alpha and beta) that are differentially expressed in tissues. We show multiple mature mRNAs in rat heart derived from alternative splicing of CPT-I beta transcripts. Two novel messages are deleted for regions of the previously described mRNA that encode membrane-spanning and regulatory domains, suggesting that the cognate isozymes will exhibit unique kinetic characteristics. (C) 1998 Published by Elsevier Science B.V. All rights reserved.