Genistein, a natural isoflavanoid phytoestrogen, is thought to be the active ingredient in soy that possesses breast cancer preventive properties. The molecular mechanisms that are involved in its cancer preventive properties have not been completely understood. The present study is designed to investigate the mechanism involved in the inhibitory action of genistein in MCF-7 cells. Genistein at 50 and 100 microM significantly arrested the growth of MCF-7 cells at G2/M phase (P<0.05) and decreased at the proliferative S phase (P<0.05). Using cDNA microarray technology, genes differentially regulated by genistein were identified. In particular, as confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR), genistein up-regulated heat shock protein 105 (HSP) mRNA and down-regulated mRNA expression of serum response factor (SRF), estrogen receptor (ER) alpha, disabled homolog 2 (DOC 2) and recombination activation gene 1 (RAG-1). Using real time RT-PCR, we have shown that HSP and SRF mRNA were both regulated by genistein in a time- and dose-dependent manner; however, it appears that only the effect of genistein on SRF mRNA, but not HSP mRNA expression, can be partially abolished by cotreatment with estrogen antagonist ICI 182,780. Western blotting analysis showed that the expressions of the ERalpha and SRF protein decreased significantly with genistein treatment (P<0.05). These results suggest that the inhibitory action of genistein on human breast cancer cells appears to be complex and is only partially mediated by the alteration of estrogen receptor-dependent pathways.