Chronological nutrition is based on biological clocks that include clock genes and telomeres. Clock genes predict the day/night cycle to regulate both physical and mental activity in best condition, and prevent lifestyle-related diseases. Telomeres, the repeated series of DNA sequences that cap the ends of chromosomes, become shorter during cell division, thus determine lifespan of the individuals and organs. Even when dietary intake and exercise are adequate, disturbance of diurnal rhythm results in hypertension and hyperglycemia. Human activity is driven by NADH and ATP produced from nutrients, and the resulting NAD and AMP prevent telomere shortening by activating enzymes called SIRT1 and AMPK, respectively. Both enzymes collaborate in activating the master regulator PGC-1α that prevents oxidative stress and obesity. Physical activity increases PGC-1α and releases a hormone irisin from muscle that also prevents obesity. The dietary habit conforming good chronological nutrition are as follows: take nutritionally balanced breakfast every morning, distribute energy intake in the ratio breakfast: lunch: dinner = 3:3:4, and avoid dinner later than 21 o’clock or take earlier light dinner. Slow feeding and the intake of vegetables before carbohydrate are recommended to prevent rapid blood sugar increase. Regular 7 hour sleep is essential for the removal of metabolic wastes by “brain glymph system” to prevent dementia. The homeostatic and hedonic feeding and daily activity are controlled by human brain. Thus, lifestyle-related diseases will be prevented by moderation following the principles of chronological nutrition, irrespective of risk gene polymorphism.