Prostate cancer is the second leading cause of cancer related deaths in men in the United States and for many years the treatment results for metastatic prostate cancer have been disappointing. Our previous studies have shown that genistein elicits pleiotropic effects on prostate cancer cells; however, its role in invasion and metastasis has not been fully elucidated. In order to better understand the precise molecular mechanism(s) by which genistein exerts its effects on PC3 cells, we have utilized cDNA microarray to interrogate 12558 known genes to determine the gene expression profile altered by genistein treatment. We found a total of 832 genes which showed >2-fold change after genistein treatment. Among these genes, we found down-regulation of 11 genes (MMP-9, protease M, uPAR, VEGF, neuropilin, TSP, BPGF, LPA, TGF-beta2, TSP-1, PAR-2) and up-regulation of two genes (connective tissue growth factor, connective tissue activation peptide), which are related to angiogenesis, tumor cell invasion and metastasis. Reverse transcription-polymerase chain reaction, Western blot, and zymographic analysis were conducted to confirm the data of microarray at the level of mRNA, protein, and biological function. The results were in direct agreement with the microarray data. From these results, we conclude that genistein down-regulates the transcription and translation of genes critically involved in the control of angiogenesis, tumor cell invasion and metastasis, suggesting the possible therapeutic role of genistein for metastatic prostate cancer. Thus, genistein-induced alternations of gene expressions may be exploited for devising chemopreventive or therapeutic strategies, particularly for chemosensitization of metastatic prostate cancer to existing chemotherapeutic agents.