The sequencing of plant genomes which was completed a few years ago for Arabidopsis thaliana and Oryza sativa is currently underway for numerous crop plants of commercial value such as maize, poplar, tomato grape or tobacco. In addition, hundreds of thousands of expressed sequence tags (ESTs) are publicly available that may well represent 40–60% of the genes present in plant genomes. Despite its importance for life sciences, genome information is only an initial step towards understanding gene function (functional genomics) and deciphering the complex relationships between individual genes in the framework of gene networks. In this chapter we introduce and discuss means of generating and identifying genetic diversity, i.e., means to genetically perturb a biological system and to subsequently analyse the systems response, e.g., the changes in plant morphology and chemical composition. Generating and identifying genetic diversity is in its own right a highly powerful resource of information and is established as an invaluable tool for systems biology.