Calcitonin (CT) enhances calcium excretion by inhibition of renal tubular calcium resorption, but the precise functions of CT remain poorly understood. We carried out in situ hybridization (ISH) for the calcitonin receptor (CTR) to evaluate the site that expresses CTR mRNA in the rat kidney. The intense signal was observed in the straight tubule of the cortex and the outer stripe of the outer medulla, but not in the inner medulla. A less intense signal was observed in the convoluted and collecting tubules, glomeruli, and renal tubule of the inner stripe of the outer medulla. Although CTR expression in the proximal straight tubule was suggested based on the physiological evidence, CTR localization was not proven. We demonstrated CTR expression in the proximal straight tubule, in addition to the distal straight tubule reported in previous studies using autoradiography. It was not possible to distinguish two CTR isoforms (C1a and C1b) by ISH, because a new probe recognized the common sequence of these isoforms. As only C1a was confirmed in kidney by RT-PCR, it seems reasonably certain that the ISH signal is of the C1a type. This new CTR probe can be an important tool for analyzing CTR expression in various tissues.