The demand for the production of valuable secondary metabolites is increasing rapidly. While many metabolites can be directly extracted from intact plants, others are routinely produced using cell or organ cultures. The latter, also called Hairy roots when generated through the transformation with the bacterium Agrobacterium rhizogenes, are also amenable to molecular modifications. Similar to intact plants metabolic pathways can be altered by introducing homologous or foreign genes. The better the knowledge of a given pathway, the more efficient will be the genetic alteration. Some of the general requirements for metabolic engineering of secondary metabolites will be discussed together with methodological considerations, especially the analysis of secondary metabolites and also the transformation methods. In addition, some examples for successful establishment of transgenic plants for metabolite production will be described. Finally, some alternative plant production systems will be discussed.