Circadian rhythm involves physical, mental and behavioral changes that follow a daily cycle and oscillate within a period about 24 hours per day. The mechanism of resetting of the clocks with varying time zones and cues occurs in organisms from bacteria to humans. It is the result of evolution – wakefulness during the day (light) and sleeping during the night (dark). The daily variations are coordinated by a master hypothalamic clock (the suprachiasmatic nucleus) and by the peripheral oscillators. They are susceptible to environmental factors such as the light/dark shift or feeding. This overview article summarizes current knowledge about the effect of nutrition on the circadian clock. Mutations in the clock genes are associated with clock mechanism disorders and with changes in adipocyte metabolism. Recent technological advancementes have led to a tremendous growth in the collective knowledge of the human microbiome. Examination of gut microbiota showed differential diurnal variations in the microbial structure and function dependent upon dietary composition. Chronobiology and chrononutrition have been gaining importance over the past 30 years. They are emerging disciplines that build on the intimate relation between endogenous circadian (24-h) rhythms and metabolism.