The present work describes the formation of Pegylated polyurethane and Lysine-coated polyurea nanoparticles obtained from O/W nano-emulsions via an interfacial polycondensation process in the aqueous solution/polysorbate 80/diisocyanate/medium chain triglyceride systems. The initial nano-emulsions were prepared using the phase inversion composition (PIC) method. Dynamic light scattering studies revealed the changes in the particle size occurring during the process of nanoparticle formation. Well-defined polymeric nanoparticles with a small particle diameter (below 80 run) and low polydispersity index were obtained using a highly hydrophilic component (polyethylene glycol or lysine) and an aliphatic diisocyante monomer. FT-IR and AFM studies showed that the polymeric matrix of nanoparticles was built by copolymers derived from reaction between the diisocyanate and the hydroxyl groups of both nonionic surfactant and the highly hydrophilic component. Pegylated-polyurethane and lysine-coated polyurea nanoparticles designed in this study are promising tools for future applications in biomedical sciences.