The transgenic hairy root culture has revolutionized the role of tissue culture of plants in the synthesis of secondary metabolites. It was shown that hairy roots in the most cases exhibit higher biosynthetic capacity for secondary metabolite production comparing to the non-transgenic roots. A big number of medicinal compounds have been produced using this approach. However, the mechanism of influence of T-DNA genes on secondary metabolite production is not completely understood. The stimulatory effect of single rol genes (rolA, rolB, rolC) on secondary metabolite production was demonstrated for a number of plant species that are widely used in pharmacology. It is interesting to note that these rol genes are present in naturally transgenic Linaria, Ipomoea, and Nicotiana plants. Many species from these genera are used as medicinal. Besides, naturally transgenic plants could be a good model for study of possible evolutionary function of rol genes in the control of secondary metabolites for plant protection.