Silicon increases the resistance of rice (Oryza sativa) to the rice blast pathogen Magnaporthe oryzae. This study described the relationship between silicon and M. oryzae in terms of whole-genome gene expression. By assessing gene expression patterns in the rice cultivar Monko-to using microarray technology, the physiological basis for silicon-induced resistance was investigated. Silicon amendment resulted in the differential regulation of 221 genes in rice without being challenged with the pathogen. This means that silicon had an observable effect on rice metabolism, as opposed to playing a simple passive role in the resistance response of rice. Compared with control plants, silicon-amended rice differentially regulated 60% less genes, implying that silicon affects the rice response to rice blast infection at a transcriptional level.