Food factors, such as amino acids, vitamins, and polyphenols, have been reported to exert biological effects through a system that senses food factors. However, how food and its components affect food factor sensing (FFS) systems remains largely unknown. Japanese are known for their longevity, to which the unique Japanese food is believed to contribute their health. We hypothesized that the promotion of health by Japanese food was due to the enhancement of food functionality by improving FFS systems. To examine the effect of Japanese soup stocks (katsuo-dashi and kombu-dashi) on FFS-related gene expression in mice, we performed DNA microarray analysis. Katsuo-dashi upregulated the expression of 10 FFS-related genes in the quadriceps, induced and suppressed that of nine and two FFS-related genes in the small intestine, and increased two FFS-related genes in the perirenal fat, respectively. Kombu-dashi upregulated and downregulated the expression of 30 and one FFS-related genes in the quadriceps, induced and suppressed that of one and one FFS-related genes in the small intestine, and increased and reduced that of two and one FFS-related genes in the perirenal fat, respectively. These data suggest that Japanese soup stocks mediate FFS-related gene expressions and might regulate their sensitivity to food factors.