Among the abiotic stresses, the availability of water is the most important factor that limits the productive potential of higher plants. The identification of novel genes, determination of their expression patterns, and the understanding of their functions in stress adaptation is essential to improve stress tolerance. Amplified fragment length polymorphism analysis of cDNA was used to identify rice genes differentially expressed in a tolerant rice variety upon water-deficit stress. In total, 103 transcript-derived fragments corresponding to differentially induced genes were identified. The results of the sequence comparison in BLAST database revealed that several differentially expressed TDFs were significantly homologous to stress regulated genes/proteins isolated from rice or other plant species. Most of the transcripts identified here were genes related to metabolism, energy, protein biosynthesis, cell defence, signal transduction, and transport. New genes involved in the response to water-deficit stress in a tolerant rice variety are reported here.