Two cDNA libraries enriched for transcripts differentially expressed in plants of two rice lines with similar genetic backgrounds and same leaf blast resistance but different responses to neck blast using suppression subtractive hybridization (SSH). After differential screening and sequence analysis of the selected clones, 90 unique cDNA clones were found, of which 74 clones were with known functions according to the putative functions of their homologous genes in the database. They may be involved in pathogen response, signal transduction, transcription, etc. Expression differences of 17 out of the 26 selected cDNA clones in resistant and susceptible lines were confirmed by RT-PCR. Expression profilings of the 26 cDNA clones at the early stages after inoculation were also revealed by RT-PCR. This is the first report on the rice neck blast resistance at mRNA level and will facilitate the further study of genetic mechanism of neck blast resistance.