Specific antisense oligonucleotide probes for the alpha isoforms of the catalytic subunit (A-subunit) of calcineurin were prepared and the distribution of A alpha 1 and A alpha 2 mRNA's has been studied in rat brain using in situ hybridization histochemistry. Clear regional differences have been observed for the A alpha 1 and A alpha 2 isoforms. The predominant form, A alpha 1, was found to be preferentially expressed in the caudate putamen, the pyramidal cell layer of the hippocampus, specific cortical cell layers, the cerebellar granular cell layer and some other brain areas. On the other hand, the A alpha 2 isoform, although being generally less abundant than A alpha 1, gave an intense autoradiography signal in the dentate gyrus of the hippocampus and was the major transcript in the amygdala, the superior and the inferior colliculus, the central gray matter and the reticular formation. These regional differences might reflect specific functions exerted by the two alternatively spliced isoenzymes in the CNS and opens the perspective of interfering with defined calcineurin-dependent signal transduction pathways using isoform-specific compounds.