Suspension arrays for protein-based assays have been developed using shape-coded poly(ethylene glycol) (PEG) hydrogel microparticles to overcome the problems with current systems which use color-coded rigid microparticles as protein supports. Various shapes of hydrogel microparticles were fabricated by a two-step process consisting of photopatterning and flushing using a poly(dimethylsiloxane) (PDMS) channel as a molding insert. Hydrogel microparticles with lateral dimensions ranging from 50 to 300 mu m were fabricated using different molecular weights of PEG (700, 3,400, and 8,000 Da), by which the water content and swelling behavior of the hydrogel microparticles could be controlled. Protein-entrapped hydrogel microparticles were prepared in a suspension array format, and PEG hydrogel could encapsulate proteins without deactivation for a week due to its high water content and soft nature. The sequential bienzymatic reaction of hydrogel-entrapped glucose oxidase (GOX) and peroxidase (POD) was successfully investigated using fluorescence detection, demonstrating one possible application of suspension arrays. Furthermore, a mixture of two different shapes of hydrogel microparticles containing GOX/POD and alkaline phosphatase (AP), respectively, was prepared and the shape-coded suspension array was used for simultaneous characterization of two different enzyme-catalyzed reactions.