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To make the most of the exponentially accumulating genomic data, however, it is crucial to analyze the proteins encoded by these genomic sequences. In this study, we adopted an engineered cell\u2010free protein synthesis system for large\u2010scale expression screening of an expression sequence tag (EST) library of <jats:italic>Clonorchis sinensis<\/jats:italic> to identify potential antigens that can be used for diagnosis and treatment of clonorchiasis. To allow high\u2010throughput expression and identification of individual genes comprising the library, a cell\u2010free synthesis reaction was designed such that both the template DNA and the expressed proteins were co\u2010immobilized on the same microbeads, leading to microbead\u2010based linkage of the genotype and phenotype. This reaction configuration allowed streamlined expression, recovery, and analysis of proteins. This approach enabled us to identify 21 antigenic proteins. \u00a9 2017 American Institute of Chemical Engineers Biotechnol. 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