Epidemiological studies have indicated that phytoestrogen has a preventive effect on breast cancer development. However, controversial results have been reported suggesting these compounds have ambivalent effects on breast tissue. Here, we report a transgenerational study conducted on female Wistar rats fed a diet enriched with phytoestrogen. Using a pangenomic microarray approach, a transcriptomic study was performed on mammary glands extracted from the animals. Gene expression was examined at 3 ages: 3, 18 and 24 months. The F1 generation did not express the same genes as the F0 control generation fed the same diet. This effect increased with animal age: in 3-, 18- and 24-month-old rats, 293, 441 and 2868 differentially expressed genes were respectively observed. These results suggest that long-term exposure to isoflavones may play a key role in gene regulation. Additionally, epigenetic patterns were found to be affected by DNA-methyltransferase and histone-deacetylase expression.