Genistein has been implicated for its anti-atherogenic effects. We investigated the molecular mechanisms behind the impact of genistein on expression of LDLR, the receptor for LDL-cholesterol, and related signaling pathways in HepG2 cells. Genistein increased mRNA and protein levels of LDLR in a time-dependent manner. In order to find out the effects of genistein on the transcriptional levels, a luciferase reporter construct containing LDLR promoter (pLDLR-luc) was constructed and examined for its response to genistein. Genistein increased the reporter activity but failed to increase transcriptional activity when sterol-regulatory element (SRE) in the LDLR promoter was deleted. Genistein increased nuclear translocation of SREBP-2 and DNA binding activity of SREBP-2 to LDLR promoter by chromatin immunoprecipitation assay (CHIP). Pre-treatment of 4-(2-aminoethyl) benzenesulfonyl fluoride (AEBSF), serine protease inhibitor, prevented the effects of genistein while brefeldin A causing the fusion of the endoplasmic reticulum (ER) and the Golgi apparatus did not, suggesting that genistein may have an effect on SREBP-2 trafficking from the ER to the Golgi apparatus. Insig-1 protein levels were not changed by genistein. Among mitogen-activated protein kinases (MAPK), genistein phosphorylated JNK but not p38 and ERK signals. JNK inhibitor (SP600126) abolished genistein-stimulated levels of LDLR and nuclear SREBP-2. To minimize the effects of c-Jun, a transcription factor activated by JNK signals, a truncated LDLR luciferase construct that contained SRE but lacked the c-jun putative binding site was constructed. Genistein still was able to boost the transcriptional activity of the truncated LDLR construct. All the genistein effects were abolished by the addition of cholesterol. In conclusion, genistein has the anti-atherogenic effects by activating JNK signals and SREBP-2 processing, which is followed by up-regulation of LDLR. However, the beneficial effects of genistein could be affected by the amount of cellular cholesterols.