Barley yellow dwarf virus (BYDV) caused one of the most serious virus diseases of wheat (Triticum aestivum) worldwide. The wheat-Thinopyrum intermedium translocation line YW642 carries BYDV resistance gene Bdv2. To explore resistant wheat resistome in response to BYDV infection, we used Affymetrix GeneChip® Wheat Genome Arrays to analyze transcriptomes of YW642 and its susceptible parent Zhong8601 at 12 and 72 h postinoculation with BYDV compared to mock-inoculated controls. Relative to mock-inoculated control, 335 defense-related transcripts were upregulated in BYDV-inoculated YW642, among which 70 were upregulated only in BYDV-inoculated YW642 but not in BYDV-inoculated Zhong8601 through clustering analysis. Additional analysis using BYDV-inoculated Zhong8601 as reference revealed that 59 defense-related transcripts were upregulated in BYDV-inoculated YW642. Comparison of these upregulated defense transcripts obtained via the two analysis ways indicated that 19 overlapped defense-related transcripts were highly expressed in BYDV-inoculated YW642 relative to BYDV-inoculated Zhong8601 and mock-inoculated YW642, which likely are significant factors in Bdv2-mediated defense response to BYDV. High expression of some resistance homologous genes, pathogen-associated molecular pattern-triggered immunity-related genes, ABC transporter genes, pathogenesis-related protein genes, and genes in reactive oxygen species, phospholipid signaling, and jasmonic acid-signaling may contribute to Bdv2-mediated defense response to BYDV.