SUMMARY Generally, Magnaporthe oryzae, the causal agent of rice blast disease, is considered to be a typical leaf-infecting plant pathogenic fungus. However, it was recently reported that M. oryzae shares many characteristics in common with root-infecting pathogens and indeed was able to infect roots. Here, we report on studies testing for the capacity of roots of rice and barley to resist infections with M. oryzae. We established that roots of rice plants were colonized by M. oryzae in a manner which is different from the gene-for-gene specificity seen in leaves for the same genotypes. Furthermore, treatment of rice seedlings with benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), a chemical that protects leaves effectively against blast by conditioning acquired resistance, was not able to prevent colonization of roots by M. oryzae although a reduction in disease levels was observed. Moreover, BTH was not able to protect barley roots against infection with M. oryzae. Taken together, our results suggest that although roots show intrinsic variation in their ability to resist colonization by M. oryzae, neither gene-for-gene incompatibility nor aquired resistance are as effective at blocking the pathogen as they are in leaves.