Subtractive hybridization analysis of region-specific gene expression in brain has demonstrated a mRNA species enriched in rat hypothalamus [K.M. Gautvik, L. de Lecea, V.T. Gautvik, P.E. Danielson, P. Tranque, A. Dopazo, F.E. Bloom, J.G. Sutcliffe, Proc. Natl. Acad. Sci. USA 93 (1996) 8733-8738.]. We here show that this mRNA encodes a Ca(2+)/calmodulin-dependent (CaM) kinase belonging in the CaM kinase I beta subgroup. cDNA analysis showed that this enzyme was differentially spliced into two isoforms (designated beta1 and beta2) with distinct C-termini. The C-terminal of the translated CaM kinase I beta2 protein (38.5 kDa molecular size), contained 25 amino acid residues not present in the beta1 isoform. The two isoforms were differentially developmentally regulated, with the beta1 isoform being present in rat embryos from day 18 and the beta2 isoform being present from day 5 postnatally. In situ hybridization analysis of adult rat CNS showed CaM kinase I beta2 mRNA being enriched in the hypothalamus and the hippocampal formation. Expression was also observed in a number of ventral limbic structures and in the thalamus. Northern blot analysis showed additional expression of multiple beta2 isoforms in heart and skeletal muscle. The human mRNA showed a similar distribution. Our data suggest that the two isoforms of CaM kinase I beta, created by a splicing process occurring within a week around birth, may have distinct pre- and postnatal functions in a distinct set of CNS neurons and excitable tissues.