Pituitary adenylate cyclase-activating peptide is densely distributed in the suprachiasmatic nucleus, which functions as the circadian pacemaker. A receptor for pituitary adenylate cyclase-activating peptide, denoted as PAC(1), exists in six variant forms. We used reverse transcriptase-polymerase chain reaction to identify the PAC(1) variants that are expressed in the suprachiasmatic nucleus. Dominant variant forms of PAC(1) in the suprachiasmatic nucleus were PAC(1)short, PAC(1)hip, and PAC(1)hop1. By in situ hybridization, we examined 24-h profiles of mRNAs for the identified receptor variants in the suprachiasmatic nucleus in constant darkness and during the light-dark cycle. In constant darkness there were clear circadian rhythms in PAC(1)short mRNA with a peak at circadian time 4 but no rhythmicity was observed in PAC(1)hip mRNA or PAC(1)hop1 mRNA. In light-dark cycles, on the other hand, PAC(1)hip mRNA displayed a bimodal rhythm with troughs at zeitgeber time 4 and 16 but PAC(1)hop1 mRNA stayed constant during the day. These results suggest that PAC(1) splice variants are differentially regulated in the rat suprachiasmatic nucleus.