Transformed roots in axenic culture would prove to be a good model for the study of the aspects of secondary metabolism. They are morphologically differentiated and have the advantage of high growth in the liquid standard media without growth regulators. Hairy root cultures can express root-specific pathways and have stable production of alkaloids, polyacetylenes, sesquiterpenes, naphthoquinones and other natural products. They can also convert xenobiotics into bioactive metabolites. Thus, new compounds not found in the parent plants could be obtained. Despite encouraging results, no commercial application of hairy root cultures for production of secondary metabolites have been developed, so far. A lot of further work is required to optimize bioreactor design for differentiated plant organ and to improve productivity of hairy roots.