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Circadian rhythms are generated by the circadian clock, a self-sustained internal timing system that exhibits 24-h rhythms in the body. Many metabolic, cellular, behavioral and physiological processes are regulated by the circadian clock in coordination with environmental cues. The present study is a comprehensive review of the currently existing evidence concerning the relationship between circadian rhythms and sleep, metabolic, and cardiovascular disorders. We thoroughly searched the online databases PubMed, Scopus, and Web of Science to find the existing clinical studies from the last twenty-three years (2000–2023). Circadian misalignment was found to be associated with an increase in the risk of metabolic disorders, cardiovascular diseases, and obesity, as well as inadequate sleep quality. In this review article, all the included studies had a strength protocol design and all of them were conducted on humans. However, the most common limitations of them were the small sample size and the short time of the intervention. In conclusion, managing the factors that disrupt the optimal function of central and peripheral clocks can help to reduce the risk of metabolic and cardiovascular diseases, improving also sleep quality. Future studies should further explore the underlying mechanisms of the interconnections between circadian clocks and sleep, metabolic, and cardiovascular disorders. This may provide new opportunities for advance chronotherapy approach.