Calcitonin receptor (CTR) has been identified in bone, kidney and brain, but precise tissue distribution and cellular localization remain to be established. In this study, we carried out in situ hybridization (ISH) analysis of CTR in rats and found intensive signals in exocrine glands, including salivary gland, exocrine pancreas and fundic glands of the glandular stomach, and epithelia of the seminal vesicle and prostatic glands. On the other hand, no signals were seen in the mesenchymal tissue including muscle, and connective and hematopoietic tissues. RT-PCR analysis showed that both CTR isoforms, C1a and C1b, were expressed in the central nervous system, only C1a isoform in the digestive, respiratory, urinary, reproductive and endocrine systems, and neither isoform in the mesenchymal tissue and hematopoietic tissues. These results showed that expression of CTR isoforms varies among various tissues, suggesting that CT functions through different mechanisms.