The primary route of infection for fire blight pathogen Erwinia amylovora in the spring is through the blossom, leading to blossom blight. Blossom blight phase is the key stage for fire blight control and blossom represents one of the most active sites of resistance to fire blight pathogen. To identify genes in apple blossom that may be involved in fire blight resistance or genes may be specific to virulence factors such as type III secretion system (T3SS), DspE and amylovoran (ams), gene expression profiling was conducted using an oligo array containing 40,000 unique apple genes. Blossoms of the susceptible 'Gala' cultivar were harvested from apple orchard and inoculated with E. amylovora wild type and various mutant strains, including T3SS, ams and dspE. Blossom tissues were collected at 2, 8 and 24 h post inoculation. Our results showed that a total of 3500 genes were found to be significantly modulated in response to WT strain compared to un-inoculated control. 770, 855, and 1002 genes were up-regulated, whereas 748, 1024, and 1455 genes were down-regulated at 2, 8 and 24 h, respectively. These genes were classified based on their functional categories and the majority of the differentially regulated genes was involved in metabolism, signal transduction, defense, transport and stress response. In addition, differentially expressed genes were also identified by comparing WT versus mutants-challenged blossoms. More than 150 genes were commonly modulated by comparing WT versus T3SS and dspE mutant-challenged blossoms at three time points, suggesting these genes may be specific to T3SS, and indicating that T3SS may play a significant role in the early stage of infection. Interestingly, relatively small numbers of genes were identified after comparing WT versus ams mutant strain, indicating that amylovoran may not play a major role in the early stage of pathogenesis.