1. An internal time-measuring mechanism which helps to adjust an organism's daily activities, seasonal activities, or both in response to environmental cues.
2. The internal mechanism of an organism that regulates circadian rhythms (daily cycles of activities) observed in many living organisms and various other periodic cycles.

The mechanism of the biological clock has long proved elusive; however, a molecular basis for such a clock in the fruit fly Drosophila has been discovered, and similar mechanisms may well apply in other organisms.

It is based on the cyclical rise and fall in the concentrations of certain proteins which form part of a negative feedback loop that controls transcription of their own genes.