Genistein, the primary isoflavone component of soy, consumed in diet during the prepubertal period suppresses chemically induced mammary cancer in rats. The current study used two-dimensional gel electrophoresis (2-DE)/MS-based proteomic technology to identify proteins responsible for genistein breast cancer protection In Vivo. Female offspring were exposed via lactating dams treated with 250 mg genistein/kg AIN-76A diet from days 1 to 21 postpartum (prepubertal period). Mammary glands were collected at 21 and 50 day of age and subjected to 2-DE/MS and immuno-blot analyses. Twenty-three proteins were determined to be differentially regulated (p < 0.05) and identified using 2-DE, followed by MALDI-TOF/TOF or LC-ESI-MS/MS. Five of these proteins were validated by immuno-blots. Annexin A2 was significantly increased at 21 days yet found to be decreased at 50 days. Fetuin B was found to be unchanged at day 21 but increased at day 50. Phosphoglycerate kinase 1 (PGK1) was unchanged at day 21 but decreased at day 50. Gelsolin was increased at day 21 but not at day 50. Protein disulfide-isomerase A3 (PDIA3) was decreased at day 21 and unchanged at day 50. Also, we found that vascular endothelial growth factor receptor 2 (VEGF-R2) and epidermal growth factor receptor (EGF-R) were decreased in mammary glands of 50-day-old rats treated prepubertally with genistein. This study demonstrates the usefulness of proteomics for the discovery of key proteins involved in signaling pathways to understand genistein mechanisms of action in breast cancer prevention.