The function of bacterial-blight resistance gene Xa3/Xa26 in rice is influenced by genetic background; the Oryza sativa L. ssp. japonica background can increase Xa3/Xa26 expression, resulting in an enhanced resistance. To identify whether Xa3/Xa26 transcript level is the only factor contributing to genetic background-controlled resistance, we screened an F2 population that was developed from a cross between Oryza sativa L. ssp. indica and japonica rice lines and was segregating for Xa3/Xa26, and compared the expression profiles of a pair of indica and japonica rice lines that both carried Xa3/Xa26. Eight quantitative trait loci (QTLs), in addition to Xa3/Xa26, were identified as contributing to the bacterial resistance of this population. Four of the eight QTLs were contributed to the japonica line. The resistance of this population was also affected by epistatic effects. Some F2 individuals showed significantly increased Xa3/Xa26 transcripts, but the increased transcripts did not completely correlate with the reduced disease in this population. The analysis of the expression profile of Xa3/Xa26-mediated resistance using a microarray containing approximate 7,990 rice genes identified 44 differentially expressed genes. Thirty-five genes were rapidly activated in the japonica background, but not in the indica background, during disease resistance. These results suggest that multiple factors, including the one resulting in increased Xa3/Xa26 expression, may contribute to the enhanced resistance in the japonica background. These factors can cause a variation in gene expression profile that differs from that in the indica background during disease resistance.