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Recently, the field of epigenetics has been intensively studied in relation to nutrition. In our study, the gene expression patterns of histone deacetylases (<i>HDAC</i>s), which regulate the stability of histone proteins, and DNA methyltransferases (<i>DNMT</i>s), which regulate DNA methylation, were determined in mice. The animals were fed a human-equivalent dose of the aqueous extract of fruit seeds and peels, which is rich in flavonoids and polyphenols, for 28 days and then exposed to the carcinogen 7,12-dimethylbenz(a)anthracene (DMBA). The concentrations of trans-resveratrol and trans-piceid were determined in the consumed extract by HPLC and were 1.74 mg/L (SD 0.13 mg/L) and 2.37 mg/L (SD 0.32 mg/L), respectively, which corresponds to the consumption of 0.2–1 L of red wine, the main dietary source of resveratrol, in humans daily. Subsequently, 24 h after DMBA exposure, the expression patterns of the <i>HDAC</i> and <i>DNMT</i> genes in the liver and kidneys were determined by qRT-PCR. The DMBA-induced expression of the tested genes <i>HDAC1</i>, <i>HDAC2</i>, <i>DNMT1</i>, <i>DNMT3A</i> and <i>DNMT3B</i> was reduced in most cases by the extract. It has already been shown that inhibition of the <i>DNMT</i> and <i>HDAC</i> genes may delay cancer development and tumour progression. We hypothesise that the extract studied may exert chemopreventive effects.