To understand plant-pathogen interactions, a complete set of hot pepper genes differentially expressed against pathogen attack was isolated. As an initial step, hundreds of differentially expressed cDNAs were isolated from hot pepper leaves showing non-host resistance against bacterial plant pathogens (Xanthomonas campestris pv. glycines and Pseudomonas syringae pv. syringae) using differential display reverse transcription polymerase chain reaction (DDRT-PCR) technique. Reverse Northern and Northern blot analyses revealed that 50% of those genes were differentially expressed in pepper leaves during non-host resistance response. Among them, independent genes without redundancy were micro-arrayed for further analysis. Random EST sequence database were also generated from various cDNA libraries including pepper tissue specific libraries and leaves showing non-host hypersensitive response against X. campestris pv. glycines. As a primary stage, thousands of cDNA clones were sequenced and EST data were analyzed. These clones are being spotted on glass slide to study the expression profiling. Results of this study may further broaden knowledge on plant-pathogen interactions.