Plant abiotic stress responses are a major yield-limiting factor in agriculture and thereby in the production of food, feed and fibre. Recent technology developments allow studies of such stress responses at a global molecular scale using omics data (metabolome, proteome, transcriptome and more). Significant progress has been made in statistical, mathematical and informatics driven analysis of omics data. Genes, proteins and metabolites can now be classified, categorized and linked at a genomic scale, and network-based analysis of various biological processes is becoming reality. However, in order to gain a complete overview of all processes and active networks in each cell type of the plant at all developmental stages and under all types of environmental variation, data production needs to become feasible at a significantly more massive scale. Systems biology studies the organization of system components and their networks, with the idea that unique properties of a system can only be observed through study of the system as a whole. A system-based analysis can involve multiple scales, ranging from single cells, tissues, organs to whole organisms. One of the foundations of systems biology is the analysis of networks of interacting and interdependent components that produce the system's unique properties. Network analysis provides intuitive ways for omics data visualization, as it reduces the intrinsic complexity of such data. In this chapter we discuss systems biology as a promising tool to study plant stress responses. We list various network and visualization tools available to biologists, to help them analyse high throughput omics data sets.