High temperature during reproductive development is a major problem to wheat production and end-use quality in the Southern Great Plains and to wheat production in many environments worldwide. We have initiated a project to integrate genotypic (QTL), phenotypic and transcript level data to identify genes controlling reproductive stage heat tolerance in heat tolerant genotypes of wheat as it relates to yield and end-use quality maintenance. Efforts have initially focused on building recombinant inbred lines (RILs) and cDNA libraries enriched, through suppressive subtractive hybridization, for genes induced by the heat stress. The selected tissues for library construction included wheat heads and flag leaves isolated from plants subjected to heat stress at 10 days after pollination. A heat tolerant spring wheat cv Halberd, and a susceptible winter wheat cv Cutter were used as models to define the two adaptive responses to heat stress (heat avoidance (susceptible) and heat tolerance). Over 1920 unique ESTs have been sequenced. These genes include some potential regulatory proteins, heat shock proteins, lipid-transfer protein as well as many novel genes that may belong to uncharacterized pathways involved in response to heat stress. For example, a lipid transfer protein and an alpha amylase inhibitor remained stable during heat shock in heat-tolerant cultivar Halberd. These genes were also highly expressed in the most heat RILs but not in the most susceptible RILs. Further studies will link QTLs controlling heat tolerance to their regulation of discrete sets of the plants transcriptome.