To identify interactive molecules of proteins is an important process which leads to clarification of physiological characteristics or development of novel drugs. However, this process has many difficulties because we have to screen many molecules. So, the screening often becomes a rate-determining step. In this study, we aim at constructing high-throughput single cell-based system for screening of interactive molecules. We developed yeast cell surface display, yeast single cell chip, and automatic single-cell pick-up machine to screen many molecules comprehensively and easily. We constructed a combinatorial yeast library in which each yeast cell displays different peptide on its cell surface, and we screened yeast cells which interacted with a model protein, neurolysin, a close relative of cancer matrix metalloproteinase (MMP) - 2/- 9, using yeast single-cell chip and automatic single-cell pick-up machine. We succeeded to obtain cells displaying peptide which specifically interacted with neurolysin.