Plants remain a major source of diversified chemicals including primary and secondary metabolites. Low yield of therapeutically important secondary metabolites is a major constraint and hence current research is focusing on techniques of enhancement of secondary metabolites production. Agrobacterium rhizogenes is a soil bacterium which causes hairy root disease at the site of infection. This disease is characterized by speedy growing, highly branched adventitious roots. Hairy roots can be grown by in-vitro method in hormone-free culture medium. Such hairy roots are efficient means of producing secondary metabolites, transgenic plants, phytoremediation and biotransformation. Present chapter will discuss hairy root establishment, analysis, stability, scale up in bioreactors and various secondary metabolites production protocols.