We have shown that cytosolic Ca2+ concentration oscillates in circadian fashion in cultured mouse suprachiasmatic nucleus (SCN) neurons and in the in vivo Drosophila ventral lateral neurons (LNvs). Since these neurons play a critical role for the generation of behavioral rhythms, the circadian Ca2+ oscillations may mediate cellular output processes in circadian pacemaker neurons in diverse systems. To further analyze the function of clock genes for the circadian Ca2+ rhythm generations, the present study examined over-expression of Bmal1 genes or of its dominant-negative genes in cultured SCN neurons. Also, Per01 mutant flies carrying pdf-gal4/UAS-cameleon were generated to investigate the function of clock genes in the Ca2+ dynamics of Drosophila LNvs. All of these genetic manipulations caused reduction of circadian Ca2+ rhythms. Therefore, we concluded that temporal patterns of cytosolic Ca2+ concentrations are regulated by the above clock gene families in circadian pacemaker neurons. [J Physiol Sci. 2006;56 Suppl:S16]