Technical Abstract: Sheath blight caused by the fungal pathogen Rhizoctonia solani is an emerging problem in rice production worldwide. To elucidate the molecular basis of rice defense to the pathogen, two RL-SAGE libraries were made from the R. solani infected and control plants of Jasmine 85, which is moderately resistant to the pathogen. The bioinformatics analysis identified 20,233 and 24,049 distinct tags from the control and treated libraries, respectively. Among the distinct significant tags (>2 copies) from the control (11,448) and treated (11,317) libraries, 36% of them were specifically present in the infected library and 55% were shared between the two libraries. Due to sequence divergence, a moderate percentage of the control (68%) and treated (65%) library tags of Jasmine 85 matched the Nipponbare genomic sequence. Nearly half of the significant tags from both libraries matched the TIGR annotated genes as well as KOME full-length cDNAs. Among them, 42% and 7% were sense and antisense transcripts, respectively. Many novel genes related to defense and metabolism were highly expressed in the infected library. Five top copy number tags specifically up- and down-regulated transcript in the infected library were evaluated through RT-PCR. A comparison of R. solani and Magnaporthe grisea infected rice transcriptomes revealed that many novel genes had similar expression patterns in the rice plants infected by both fungal pathogens.