Genetic technologies have become a tool for achieving the desired properties of plant crops instead of traditional breeding in recent decades. They consist in artificial editing of a plant genome (genetic modification) by inserting the genes encoding desired features from the DNA of one organism in another, often unrelated, species. One of the most popular crops is soybean containing up to 38–42% of proteins in its seeds, and its most common type is GTS 40-3-2 (Monsanto Canada Inc.) line of transgenic soybean. The genetically modified soybean "Roundup Ready" is resistant to the action of herbicide "Roundup" (it continues to grow when it is cultivated with this herbicide). Therefore, the study of individual and combined effects of both factors on the free radical oxidation processes in biomolecules is very relevant. Experimental research was performed on 4-month Wistar rats to study the long-term effects of feeding with genetically modified soybean and herbicide "Roundup", both separately and together, on the rat kidneys. The results of the study showed that after 12 months of feeding with genetically modified soybean treated with herbicide "Roundup" (IV group) and receiving the herbicide with drinkable water (V group), there was an increase in the level of carbonyl derivatives in the rat kidney homogenates in the first (F0) and in subsequent generations (F1, F2) of rats. The research results showed that the highest level of carbonyl derivatives was noted in the kidneys of the third generation of rats. Along with the increase in oxidatively modified proteins in the rat kidney homogenates, there was a decrease in the content of sulfhydryl groups and proteolytic enzymes in the IV and V groups, the lowest level was observed in the third generation. The use of the same transgenic soybean variety not treated with any herbicide did not lead to an increase in the level of carbonyl derivatives and a decrease in the content of sulfhydryl groups compared to control group rats. Thus, the obtained experimental data indicate that both feeding with the genetically modified soybean treated with the herbicide and receiving the herbicide "Roundup" with drinkable water lead to the initiation of free radical processes in the kidneys of rats of all three generations and imbalance of the oxidant–antioxidant system, most notably in the third generation of rats. Such research results indicate the negative effects of the investigated factors and indicate that the herbicide "Roundup" may be accumulated in the seeds of transgenic soybean and also it may increase the oxidative modification of proteins in the rat kidneys. Hence, it is necessary to carry out a detailed study of the effects of these factors on histochemical changes in the kidney and liver structure and an investigation of antioxidant enzyme activity in these organs.