Circadian clocks, internal timekeepers that generate a daily rhythmicity, help organisms to be prepared for periodic environmental changes of light and temperature. These molecular clocks are transcriptional feedback loops that generate 24-h oscillations in the abundance of clock proteins. For the maintenance of this rhythm inside the core clockwork and for its transmission to downstream genes the clock proteins additionally rely on post-transcriptional and post-translational mechanisms. Thus clock proteins engage in a variety of interactions with DNA, RNA and other proteins. Based on the model organisms Drosophila melanogaster and Arabidopsis thaliana molecular principles of circadian clocks are discussed in this review.