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We developed various assay systems using protein arrays for protein profiling and determination of enzyme activities in a high-throughput manner. Protein arrays is a key technology in proteomics and serodiagnosis, since the technology allows a high-throughput and large-scale analysis of protein interactions in a small sample format. We fabricated protein arrays by immobilizing proteins or antibodies to well-type amine arrays. We developed assay systems for rapid determination of matrixmetalloproteinase (MMP)-3 activity using an array-based spectral surface plasmon resonance biosensor and fluorescence-based gelatin arrays, and these systems showed a potential for screening of MMP-3 inhibitors. We also developed an on-chip activity assay of blood coagulation factor XIII (FXIII) using fluorescence-based fibrinogen arrays and it showed a strong potential to be applied toward FXIII-related personalized medicines. In addition, fluorescence-based antibody arrays were successfully applied to identification of serological marker proteins for liver disease. Thus, protein array system, based on SPR biosensors and fluorescence detection, is useful for inhibitor screening, serodiagnosis, and personalized medicine.