The distribution of the mRNAs encoding the different isoforms of the catalytic subunit (A subunit) of calcineurin has been investigated in rat thymus and kidney using in situ hybridization histochemistry with specific antisense oligonucleotide probes. In the thymus, the mRNAs of the Aβ isoforms were the predominant transcripts and showed very intense hybridization signals in the cortical areas. The Aα mRNAs were expressed at low levels. Aβ2 mRNA was expressed at higher levels than Aβ3 mRNA, but no difference could be detected between the expression levels of Aα1 and Aα2. In the kidney, highest calcineurin A mRNA hybridization signals were found in the medulla. Signal intensities of Aα mRNAs were comparable to those of Aβ mRNAs. Aα1 mRNA level was extremely weak, and Aβ2 mRNA expression was slightly higher than Aβ3 mRNA expression. A tissue-specific distribution pattern of the alternatively spliced isoforms of calcineurin A, as suggested by these preliminary data from thymus and kidney, may be critical in understanding the toxic side-effects associated with the use of the immunosuppressive, calcineurin-inhibiting compounds cyclosporin A and FK506.