Metabolic activity in the suprachiasmatic nucleus (SCN), a center of biological rhythm, is higher during the daytime than at night. The rhythmic oscillation in the SCN is feedback controlled by the CLOCK/BMAL1 heterodimer binding to the E-box in target genes (e.g., Arg- vasopressin). Similar transcriptional regulation by NPAS2/BMAL1 heterodimer formation operates in the brain, which depends on the redox state (i.e., NAD/NADH). To clarify the metabolic function of SCN in relation to the redox state, two-dimensional electrophoresis was carried out on the mitochondrial fraction of SCN, obtained from rats kept under a light:dark cycle and constant under dim light. The electrophoretic pattern with TOF-mass spectrometry analysis revealed that enolase catalyzes the interconversion of 2-phosphoglycerate and phosphoenolpyruvate. The enolase activity, coupled with lactate dehydrogenase, was higher during the light period than that in the dark. However, enolase mRNA, analyzed by RT-PCR, showed higher levels during the dark period than in the light. The clock gene products Per2, Bmal1, Rev-erbα, and AVP mRNA in the mitochondrial fraction of SCN developed a circadian rhythm showing almost the same peak time as that in whole SCN. These mRNA rhythms ran free except for that of Rev-erbα mRNA. The results indicate that, in the glycolysis-related energy pathway, enolase might be involved in higher metabolic activity during the day than at night, at least in part.