Microencapsulation of living cells provides a novel technology to overcome various medical problems since the polymer membrane acts as an immunological barrier protecting the transplanted cells from immunorejection. It has been applied to a wide range of therapeutic treatments, such as diabetes, hemophilia, Parkinsons disease, cancer, and renal failure. By using hydrodynamic flow focusing, the diameter of the microcapsule particles formed is uniform and much smaller than that of conventional methods. Here we show the production of alginate and agarose hydrogel encapsulate particles in microfluidic devices. The hydrogel particles were coated with polyelectrolyte multilayer to control the permeability of macromolecules, and with colloidal particles to tailor the mechanical stabilities. Encapsulation of bacteria in uniform hydrogel particles will be presented.