In this study, antibody-based protein microarrays for high-throughput immunoassay were fabricated on an aldehyde-modified indium-tin oxide glass plate using the electrospray deposition (ESD) method and their characteristics were evaluated immunochemically. The microarrays were also integrated into microfluidic chips with a polydimethylsiloxane (PDMS) micro-channel to detect human cytokines, which were quantitatively analyzed with a high resolution charge-coupled device. Simultaneous detection of various antigens was performed using the microarrays with considerable sensitivity (ca. 100 pg/mL). The results of this study indicate that microfluidic chip comprising a protein microarray formed by the ESD method and a PDMS micro-channel could be easy to handle, and offers high-throughput detection of molecular biomarkers.