Abiotic stresses limit rice production across the rainfed environments, which comprise about 45% of the global rice area. Important stresses for lowland rainfed rice include submergence and salinity, while upland rice is subject to P deficiency, and water deficit. In recent years, advances in physiology, molecular biology, and genetics have greatly improved our understanding of response of rice plant to these stresses and the basis of varietal differences to tolerance. Rice has been used as a model species in molecular and genomic studies. QTLs have been identified that explain a considerable portion of observed variation, and in some cases, the genes underlying specific QTLs have been identified. Transformation has been used to assess the effects of altered expression of specific stress-related genes, allowing confirmation of the importance of particular metabolic pathways. Through expression profiling of many genes simultaneously, it has been possible to identify three types of stress-responsive gene networks: early signaling pathways, adaptive responses, and genes that reflect downstream results of damage. For crop improvement the identification of useful allelic variation for genes in the second group may be the most promising approach. Either molecular approaches or traitspecific physiological screenings can be used to search for these superior alleles. Marker-assisted backcrossing can then be applied to incorporate these alleles into agronomically superior germplasm. Here we review progress in applying molecular approaches to explore genetic variation in rice for tolerance to selected abiotic stresses.