The tau mutation is a semidominant autosomal allele that dramatically shortens period length of circadian rhythms in Syrian hamsters. We report the molecular identification of the tau locus using genetically directed representational difference analysis to define a region of conserved synteny in hamsters with both the mouse and human genomes. The tau locus is encoded by casein kinase I epsilon (CKIɛ), a homolog of the Drosophila circadian gene double-time. In vitro expression and functional studies of wild-type and tau mutant CKIɛ enzyme reveal that the mutant enzyme has a markedly reduced maximal velocity and autophosphorylation state. In addition, in vitro CKIɛ can interact with mammalian PERIOD proteins, and the mutant enzyme is deficient in its ability to phosphorylate PERIOD. We conclude that tau is an allele of hamster CKIɛ and propose a mechanism by which the mutation leads to the observed aberrant circadian phenotype in mutant animals.Daily rhythms in biochemical, physiological, and behavioral processes are regulated by biological clocks (1, 2). In natural conditions, the endogenous circadian rhythms that are generated by these clocks are synchronized (entrained) to the 24-hour cycles of the external world by time cues such as the daily light/dark cycle (2). While these clocks are found in organisms as divergent as cyanobacteria, plants, fruit flies, and mammals, there is an extraordinary degree of evolutionary conservation of the underlying generative molecular mechanisms (3-9). The first mammalian circadian gene, Clock, was cloned and characterized in mouse (10-12). Clock encodes a novel member of the basic helix-loop-helix (bHLH) PER-ARNT-SIM (PAS) family of transcription factors. Shortly following the cloning of Clock, three mouse Period orthologs, denoted mPer1 (13,14), and mPer3 (18, 19), as well as a Timeless (mTim) ortholog, were cloned (20)(21)(22)(23)(24). At the same time, another gene, BMAL1 (25), was found to encode the protein dimerization partner for CLOCK (26), and together the CLOCK/BMAL complex was shown to transactivate mPer1 via conserved E-box elements found in the promoters of Drosophila and mouse period genes (26-28). Finally, in Drosophila and mammals, the negative feedback effects of PER and TIM were shown to act at the level of the CLOCK/BMAL complex (20, 28) in a surprisingly direct manner (29, 30).