Molecules derived from plants make up a sizeable proportion of the drugs currently available on the market. These include a number of secondary metabolite compounds the monetary value of which is very high. New pharmaceuticals often originate in nature. Approximately 50% of new drug entities against cancer or microbial infections are derived from plants or micro-organisms. However, these compounds are structurally often too complex to be economically manufactured by chemical synthesis, and frequently isolation from naturally grown or cultivated plants is not a sustainable option. Therefore the biotechnological production of high-value plant secondary metabolites in cultivated cells is potentially an attractive alternative. Compared to microbial systems eukaryotic organisms such as plants are far more complex, and our understanding of the metabolic pathways in plants and their regulation at the systems level has been rather poor until recently. However, metabolic engineering including advanced multigene transformation techniques and state-of-art metabolomics platforms has given us entirely new tools to exploit plants as Green Factories. Single step engineering may be successful on occasion but in complex pathways, intermediate gene interventions most often do not affect the end product accumulation. In this review we discuss recent developments towards elucidation of complex plant biosynthetic pathways and the production of a number of highvalue pharmaceuticals including paclitaxel, tropane, morphine and terpenoid indole alkaloids in plants and cell cultures.