Arabidopsis thaliana is a successful model plant for studying wide-ranging topics including plant development, genetics and pathogen resistance. In addition, significant research has been conducted in the area of secondary metabolite biochemical genetics. The secondary metabolites in Arabidopsis include glucosinolates, terpenoids, phenylpropanoids, the alkaloid-like camalexin, and other uncharacterized compounds. The genetic tools developed in studying secondary metabolite biochemistry are now being used to study how secondary metabolites control various biological processes. This includes compounds involved in plant/insect and plant/pathogen interactions, compounds preventing UV-B damage, and compounds involved in hormone homeostasis. This review will describe what light Arabidopsis is shedding on the biological and ecological importance of specific secondary metabolites.