The resistance gene Pi36 confers a stable and high level of resistance against Chinese isolates of the rice blast pathogen Magnaporthe oryzae. Quantitative real time RT-PCR was used to investigate the expression profiles of various resistance-related genes in both the Pi36/AvPi36 incompatible interactions. Among 17 members of the OsMAPK family, OsMAPK2, OsMAPK4, OsMAPK8 and OsMAPK15 were differentially expressed, as were OsWRKY30, OsWRKY32, OsWRKY64 and OsWRKY67 among the 13 OsWRKY members studied. The induction of the expression of genes from both of these families suggests that both the JA and SA pathways are involved in Pi36-mediated defence. Other genes differentially expressed included the OsbZIP transcription factors, OsNIF1 and OsNIF2, and the NPR1 homologue OsNH2, all of which were reported in the rice blast pathosystem. The involvement of these genes illustrates the complexity of the downstream signalling pathways involved in the Pi36/AvrPi36 interaction.