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We have successfully demonstrated the fabrication of biodegradable and magnetic microcapsules utilizing PDMS double emulsification devices. Specially designed 3D microfluidic channels with surface modified by a self-aligned photo-grafting process are employed to shape immiscible fluids into monodisperse W/O/W emulsions. By varying the outer and inner fluid flow-rates, the overall and core sizes of the resulting double emulsions can be adjusted accordingly. Biodegradable materials and surface-treated gamma-Fe2O3 nanoparticles are dispersed uniformly in the middle organic phase, and solidified into magnetic microcapsules once the solvent is extracted. In the prototype demonstration, microcapsules made up of poly(L-lactic acid), trilaurin and phosphocholine (DOPC) are successfully fabricated. As such, the proposed PDMS micro-devices could potentially serve as versatile encapsulation tools, which are desired for a variety of biological and pharmaceutical applications.