Rice is one of the most important staple food crop providing 35-60% of the calories to 2.7 billion people across the world. Drought stress is a serious limiting factor for rice production and yield stability across rainfed rice cultivation areas. Here we have carried out comparative genetic mapping in rice and sorghum using rice ESTs, generated from drought stressed rice seedlings of Nagina 22. ESTs are very much useful for the development of functional based markers. These EST-RFLPs were used to screen the polymorphism in selected cereals include 17 genotypes that have been used in making mapping population mainly DHLs and RILs used for drought tolerance breeding programmes across world. Of the targeted 67 putative candidate genes (EST-RFLP) of stress response and other genomic clones, 31 were mapped on to rice and 25 onto sorghum maps. Chromosomal synteny for the regions carrying these markers in rice and sorghum genomes was determined. Consensus markers that can potentially be used for identification of stress response-associated QTLs in rice and sorghum were identified.