Abiotic stresses such as extreme temperatures, low water availability, high salt and mineral deficiencies or toxicities severely diminish productivity of cereal crops. These stresses are becoming increasingly important because of the declining availability of good quality water, land degradation and community pressures to move away from chemical intervention in agriculture. Of the major cereals, wheat and barley are grown in the most hostile and consequently lowest yielding environments. Extensive genetic studies and surveys of landrace and wild germplasm have indicated extensive variation for abiotic stress tolerance but this has been difficult to exploit due to the relatively poor background knowledge of the molecular basis for stress in these species. Interconnected signal transduction pathways that lead to multiple responses to abiotic stresses have been difficult to study using traditional approaches because of their complexity and the large number of genes and gene products involved in the various defensive and developmental responses of the plant. Functional genomics is now widely seen as providing tools for dissecting abiotic stress responses in wheat and barley, through which networks of stress perception, signal transduction and defensive responses can be examined from gene transcription, through protein complements of cells, to the metabolite profiles of stressed tissues.