SUMMARY The infection of plants by pathogenic microbes and the subsequent establishment of disease involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. Root diseases have considerable economic impact but have not been characterized extensively at the molecular genetic level. Here we have used two complementary approaches-suppression subtractive hybridization and expressed sequence tag analysis of an unsubtracted cDNA library-to investigate gene expression during the early stages of colonization of wheat roots by the take-all fungus, Gaeumannomyces graminis.