The circadian clock is characterized by daily fluctuations in gene expression, protein abundance and posttranslational modification of regulatory proteins. The Drosophila PERIOD (dPER) protein is phosphorylated by the serine/threonine protein kinase, DOUBLETIME (DBT). Similarly, the murine PERIOD proteins, mPER1 and mPER2, are phosphorylated by Casein kinase I epsilon (CKIɛ), the mammalian homolog of DBT. CKIɛ also phosphorylates and partially activates the transcription factor BMAL1. Given the variety of potential targets for CKIɛ and other cellular kinases, the precise role of phosphorylation is likely to be a complex one. Biochemical analysis of these and other circadian regulatory proteins has proven to be a fruitful approach in determining how they function within the context of the molecular clockworks.