The extract from linden inflorescence is one of the pharmacognostic resources which properties are associated with the presence of flavonoids (mainly: quercetin, kaempferol, acacetin glycosides and tiliroside). Flavonoids belong to polyphenols that may play a significant role in the dietoprophylaxis of civilization diseases. These compounds have many different mechanisms of action, but most important seem to be their antioxidant properties. The aim of the present study was to investigate the influence of linden extract on a) gene expression in rat liver and determine the difference in gene expression depending on the use of hydrolyzed or non-hydrolyzed linden extract, and b) antioxidant parameters of liver tissue. Rats were fed the diet containing hydrolyzed and non-hydrolyzed extract from linden inflorescence (Tilia cordata). The administration of hydrolyzed extract increased more than two-fold the level of quercetin in rats liver when compared to non-hydrolyzed extract. The transcriptomic study performed using microarray technology revealed 344 probes regulated by linden extract and 187 probes differentiating the action of hydrolyzed from nonhydrolyzed linden extracts. The most important molecular functions of regulated genes were as follows: defense and immunity, transporter, receptor, ion channel, oxidoreductase, cytoskeletal protein and cell adhesion molecule. Among most important biological processes identified were immunity and defense, transport, homeostasis and lipid, fatty acid and steroid metabolism. The analysis of oxidative status in rats liver together with the analysis of liver transcriptomic profile suggest that the antioxidant activity of hydrolyzed linden extract is higher that the non-hydrolyzed and occurs on the level of gene expression.