A large number of plant species from several families have been successfully transformed by Agrobacterium rhizogenes and established in culture. In contrast to normal roots, the Ri-transformed root cultures are fast growing, and do not require exogenous supply of plant growth regulators in the medium to support growth. In addition, they are robust, plagiotropic, and produce the full range of secondary products characteristics of roots derived from the parent plant species. Ri transformed roots of some species synthesize novel compounds and screening and selection procedure can also be employed to improve production levels. The most interesting applications of hairy root cultures in a continuous culture program, are with secondary product pathways exclusively active in roots, and from which the product would be secreted into the medium. Large-scale secondary metabolite production from hairy roots can be achieved by using different types of bioreactors. In this review, we provide an overview of synthesis and accumulation of medicinally important secondary metabolites in Ri transformed root cultures and in Ri-transformed plants. © 2013 Springer-Verlag Berlin Heidelberg. All rights are reserved.