We examined to determine whether hepatic gene expression is affected in mice in which blood lipid levels remain unchanged fed soy protein isolate (SPI) for a short time. We also examined SPI-mediated effects in farnesoid X receptor (FXR)-deficient mice. Compared with casein, SPI affected the expression of various hepatic genes related to lipid metabolism in the wild-type mice. No effects of SPI were observed in the FXR-deficient mice, suggesting the importance of FXR. Hepatic peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) gene expression was reduced by SPI, and this might be associated with a decrease in FXR expression. Decreased FXR led to decreased expression of its target, the bile-salt export pump necessary for bile acid secretion and dietary lipid absorption. The earliest response to SPI was a decrease in hepatic sterol regulatory element-binding protein (SREBP)-1c mRNA, on day 3. SPI activated hepatic adenosine monophosphate-activated protein kinase (AMPK), which can lead to a reduction in SREBP-1c mRNA. These data indicate the importance of SREBP-1c and PGC-1α/FXR in SPI-mediated alterations in hepatic gene expression.