Nardilysin (NRDC; N-arginine dibasic convertase) is a metalloprotease of the M16 family. We have shown that NRDC has multiple functions such as an enhancer of ectodomain shedding of membrane-anchored protein and transcriptional coregulator. NRDC-deficient mice (Nrdc^-/-) show wide range of phenotypes such as hypomyelination, hypothermia, abnormal sympathetic innervation to hearts, hypotension, and bradycardia. The purpose of this study is to explore a role of NRDC in the regulation of heart rate. To this end, we have revealed the following points: (1) Intrinsic heart rate, obtained by pharmacological blocking of autonomic nervous system, was significantly reduced in Nrdc^-/-　compared with that of wild-type mice; (2) Messenger RNA levels of Cav3.1 and HCN1/4, ion channels responsible for sinus automaticity, were significantly reduced In Nrdc^-/- hearts; (3) Funny (If) current and T-type Ca current were markedly reduced in Nrdc^-/- sinus node cells; (4) Gene knockdown of NRDC in primary rat cardiomyocyte reduced mRNA levels of HCN1/4; (5) NRDC binding to the promoter region of Cav3.1 and HCN1/4 was revealed by chromatin immunoprecipitation-PCR analysis, suggesting the direct involvement of NRDC in transcriptional regulation of these ion channels; (6) Reintroduction of wild-type NRDC, but not the enzymatic inactive mutant of NRDC (E>A mutant) into NRDC-deficient cells restored the HCN1 mRNA expression, suggesting the important role of NRDC enzyme activity in the transcriptional regulation; (7) NRDC-E>A mutant knock in mice showed bradycardia and significantly reduced intrinsic heart rate. Together, our results indicate that NRDC in cardiomyocyte controls heart rate through the transcriptional regulation of ion channels critical for sinus automaticity.