Information about the effects of phytoestrogens in the liver, the main organ of metabolism, is limited. In this study we have examined the dose dependent effects of the phytoestrogen genistein (GEN) on gene expression in rat liver in comparison to the potent estrogen ethinylestradiol (EE). Special attention was paid to strain specific differences between Wistar- (WIS) and Sprague-Dawley rats (SD). EE as well as GEN stimulated the gene expression of insulin like growth factor binding protein 1 (IGFBP-1), similarly in both strains. The mRNA expression of Vitamin D dependent calcium-binding protein (CaBP9k) was stimulated by EE in both strains but more pronounced in WIS rats. Interestingly GEN stimulates CaBP9k gene expression only in SD rats. Gene expression of apolipoprotein AI (ApoAI) was not affected in both strains neither by EE nor by GEN. These results are indicative of strain specific differences in the response of liver genes to GEN or EE.