Plants produce secondary metabolites, among others, to protect themselves against microbial and herbivore attack or UV irradiation. Certain metabolite classes also function in beneficial interactions with other organisms. For example, anthocyanin pigments and terpenoid essential oils have key roles in attraction of flower pollinators. Secondary metabolites also have direct uses for man. Flavonoids and terpenoids for example have health-promoting activities as food ingredients, and several alkaloids have pharmacological activities. Controlled transcription of biosynthetic genes is one major mechanism regulating secondary metabolite production in plant cells. Several transcription factors involved in the regulation of metabolic pathway genes have been isolated and studied. There are indications that transcription factor activity itself is regulated by internal or external signals leading to controlled responses. The aim of this review is to discuss the regulation of transcription factors involved in secondary metabolism in plants at gene and protein levels, using phenylpropanoid and terpenoid indole alkaloid pathways as two well-studied examples.