Electric fields were used to control the structure of polymer composite proton conducting membranes. Under appropriate conditions, functional particles dispersed in the polymer can be aligned into chains in the direction of the applied field. The resulting composite membranes are anisotropically structured with proton conduction greatly enhanced in the alignment direction. Compared to randomly structured composites, the electric field aligned membranes have dramatically improved performance in direct methanol fuel cells. The field-induced structure results in anisotropic water swelling behavior of the membranes, with greater swelling in the direction of alignment. By tailoring the membrane structure with the electric field, the mechanical and transport properties of the membrane can be optimized for fuel cell application.