Rye (Secale cereale L.) chromatins have been used to introduce agronomically important traits into wheat (Triticum aestivum L.). Wheat-rye translocations in the form of 1RS.1AL, 1RS.1BL, 2BS.2RL have been developed for an important genetic source of disease and pest resistance. The long arm of rye chromosome 2 (2RL) has valuable genes that confer resistance to pests such as biotype L of Hessian fly, powdery mildew, leaf and stem rust. Here, we report the generation and analysis of expressed sequence tags from Hessian fly infested wheat-rye translocation. RNAs were isolated from young seedlings infested by Hessian fly. cDNA library was constructed using Clontech cDNA library construction kit. Random sequencing of candidate clones were performed. The EST clones might be useful to clone target gene sequences and would provide clues on molecular interaction between wheat and Hessian fly.