Together, temperature and water availability are the primary determinants of the global distribution of major vegetation biomes and as such have a major impact on the cultivation of temperate fruit trees. The regulation of both low temperature and water deficit stress has been widely studied in herbaceous plants using transcriptomics, proteomics, and transformation technologies. These studies have revealed stress signaling pathways, specific stress-tolerance genes, and transcriptional regulators. Using direct data or empirical approaches, biotechnology has been utilized to produce transgenic plants that have greater stress tolerance. For example, plants overexpressing the transcription factor CBF (under the control of a low-temperature-inducible promoter) have increased freezing tolerance. However, only recently, have these same approaches been used to study stress tolerance in woody plants and more specifically fruit trees. Evidence suggests that although there is a high level of conservation in mechanisms of stress tolerance between annual herbaceous plants and perennial woody plants, the perennial habit has also resulted in additional mechanisms that are specific to perennial plants. We have utilized several different global approaches to study stress tolerance in apple and peach. These include subtractive hybridization (SSH), bioinformatics analysis of ESTs derived from stress-induced cDNA libraries, and 2D Difference in-Gel Electrophoresis (DiGE) for proteomic analyses. These approaches are beginning to reveal the complexity of stress response in fruit trees and helping us develop a comprehensive understanding of stress tolerance in fruit trees. An overview of the results of these studies is presented and discussed.