Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including disease resistance. Fire blight has become increasingly more of a problem with the shift to high-density orchard planting, as the strongly dwarfing rootstocks used are generally more susceptible to the disease. The susceptibilities of the major rootstocks are relatively well established. However the influence of the rootstock on the susceptibility of the scion is less well characterized. In the spring of 2007 we performed fire blight inoculations on 3 year old trees of 'Gala' grafted on seven different rootstocks and measured the growth of the resultant cankers. 'Gala' grafted on G.30 showed the lowest rate of canker growth while 'Gala' on M.27 showed the highest rate of canker growth. Using an apple DNA microarray, we examined the gene expression patterns in greenhouse grown 'Gala' scions grafted to the same series of seven different rootstocks that we examined for the susceptibilities to fire blight. Over 100 genes were identified whose expression levels correlated with the degree of fire blight susceptibility of the scion/rootstock combinations. We will use Quantitative PCR to test these correlations in an orchard-grown population of different scion/rootstocks combinations that have been rated for fire blight susceptibility. This study demonstrates the utility of using rootstock-regulated gene expression profiling for the identification of genes associated with agriculturally important traits. These genes may be useful for apple breeding programs.