Traditionally, separation of proteins was accomplished by polyacrylamide gel electrophoresis; usually, gel structure is modified by change in concentrations of polymers in solution. This approach has worked well for many type of macromolecules; however when the electrophoretic mobility and the size of the macromolecules do no cooperate efficiently, the separation of this type of mixture become challenging. Therefore, other approaches must be identified. For example, by modifying the structure of gels by either “macro-voids” (Rills et al, 1995) or by adding nanoparticles (Thompson et al, 2008) have proven successfully in increasing separation efficiency. In this contribution, the synthesis and characterization of core/shell nanoparticles as well as dispersing them into the polyacrylamide gel matrix are described. The particles are synthesized by surfactant free emulsion polymerization and dispersed into the gels. UV-Vis spectrophotometer is used to characterize the particles. Characterization of the material structure and electrophoresis on albumin proteins is performed to confirm the effectiveness of the modified gel matrix on their separation efficiency. Comparison with other type of nanocomposite gel matrix will be also discussed.