Secondary products are small molecular weight compounds produced by secondary metabolic pathways in plants. They are regarded as non-essential for normal growth and development but often confer benefits such as defense against pathogens, pests and herbivores or the attraction of pollinators. Many secondary products affect the survival and/or behavior of microbes, insects and mammals and they often have useful pharmacological effects in humans. Most secondary products can only be obtained as extracts from medicinal plants, many of which grow slowly and are difficult to cultivate. Chemical synthesis, although possible in principle, is often impractical or uneconomical due to the complexity of their molecular structures. The large scale production of secondary products by metabolic engineering has therefore been investigated in a number of heterologous systems including microbes, plant cell/organ cultures, and intact plants. In this critical review of production platforms for plant secondary products, we discuss the advantages and constraints of different approaches and the impact of post-genomics technologies on gene discovery and metabolite analysis. We highlight bottlenecks that remain to be overcome before the routine exploitation of secondary products can be achieved for the benefit of mankind.