Circadian clock system has been widely maintained in many spices from prokaryote to mammals. "Circadian" means "approximately day" in Latin, thus circadian rhythm means about 24 hour rhythms. The earth revolves once every 24 hours, and our circadian system has been developed for adjusting to this 24 hour cycles, to get sun light information for getting their foods or for alive in birds or mammals. We have two different circadian systems so-called main oscillator located in the suprachiasmatic nucleus (SCN) of the hypothalamus, and local oscillator located in the various peripheral organ tissues such as liver, kidney and skeletal muscle. The SCN is directly entrained by light-dark information through retinal-hypothalamic tract, and then organizes local clock in peripheral tissues via many pathways including neural and hormonal functions. On the other hand, peripheral local clocks are entrained by feeding, exercise and stress stimuli through several cell signaling. Foods (protein, carbohydrate, and lipid) are important regulator of circadian clocks in peripheral tissues. Thus, controlling the timing of food consumption and food composition, a concept known as chrononutrition, is one area of active research to aid recovery from many physiological dysfunctions. In this review, we focus on molecular mechanisms of entrainment and the relationships between circadian clock systems and n-3 polyunsaturated fatty acid. We concentrate on experimental data obtained from cells or animals and humans and discuss how these findings translate into clinical research, and we highlight the latest developments in chrononutritional studies.