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Generation of circadian oscillations is based on rhythmic expression of clock genes and subsequent posttranscriptional and post-translational modifications. In addition to the central circadian oscillator - the suprachiasmatic nucleus (SCN), peripheral oscillators have been demonstrated in many tissues, including the heart and blood vessels. Melatonin mediates cyclic lighting conditions to rhythmic endocrine signal and is able to synchronize neuronal firing in the SCN via membrane receptors. Clock gene expression is melatonin sensitive in the pars tuberalis, genes cry1 and tim1 respond to single injection while neurod1 and npas4 are influenced via long lasting mechanisms. In the rat heart, melatonin phase advanced expression of per2 and bmal1 independently from its effects on the SCN. Melatonin is an important endogenous signal able to synchronize circadian oscillations in the cardiovascular system. It may be effective especially in situations when the circadian control is weakened or organism must adapt to rapid changes in rhythmic environmental conditions.