Plants have played a major role in the geochemical and climatic evolution of our planet. Today, in addition to their fundamental ecological importance plants are essential for humans as the main source of food, provide raw materials for many types of industry and chemicals for medical applications. It is thus daunting to realize how little we understand about plant systems. To date, only approximately 15% of the genes of Arabidopsis thaliana, the most explored model system for plant biologists, have been characterized experimentally. Systems biology offers the opportunity to increase our understanding of plants as living organisms, by generating a holistic view of the organism grounded at the molecular level. In this chapter, we discuss the basics of systems biology, the data and tools we need for systems research and how it can be used to produce an integrated view of plant biology. We finish with a discussion of case studies, published examples of plant systems biology research and their impact on our knowledge of plants as integrated systems.