A subtracted library was constructed from wound-treated wild rice (Oryza minuta) by suppression subtractive hybridization (SSH) in combination with mirror orientation selection (MOS). To distinguish between differentially expressed transcripts and false positive clones, DNA chips containing 960 random clones were applied as a form of reverse Northern screening. Based on the signal intensities and expression ratios obtained from experiments performed in triplicate, 371 clones were selected. ESTs produced from the subtracted library showed 63.2% redundancy, and 72% of all clones could be matched to the GenBank nonredundant database. Functional categorization placed the identified enriched genes in categories of subcellular localization, metabolism, cell rescue and defense, and transcription. These EST-related resistance mechanisms could be used in investigations into the defense mechanisms of wild species, and to provide new routes to improving the germplasm of cultivated rice.