It is known that the rolA, rolB, and rolC genes of Agrobacterium rhizogenes T-DNA affect processes of plant development and activate the synthesis of secondary metabolites in transformed plant cells. Although a synergistic activity of the rol genes on root formation is well-documented, little is known about their individual and combined action on secondary metabolism. In the present investigation, we provide evidence indicating that individual rolA, rolB, and rolC genes are capable of increasing biosynthesis of anthraquinones (AQs) in transformed calli of Rubia cordifolia. The stimulatory effect was due to the increased transcription of a key gene of AQ biosynthesis, the isochorismate synthase (ICS) gene. The strongest AQ-stimulating activity was shown for an R. cordifolia culture expressing rolB at high levels, where rolB ensured a 15-fold increase of AQ accumulation compared with the control, non-transformed calli. A tyrosine phosphatase inhibitor abolished the rolB-induced increase of AQ production, thus indicating the involvement of tyrosine (de)phosphorylation in the rolB-mediated AQ stimulation. The rolA- and rolC-expressing cultures produced 2.8- and 4.3-fold higher levels of AQs, respectively, when compared with the control calli. However, the effect of rolA, rolB, and rolC on AQ biosynthesis was not synergistic because rolA and rolC apparently attenuated the stimulatory effect of rolB on AQ biosynthesis. Therefore, the rol-gene-mediated signals that promote root formation and those which activate biosynthesis of secondary metabolites seem to have a point of divergence.