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The design of new, safe and effective nanotherapeutic systems is an important challenge for the researchers in the nanotechnology area. This study describes the formation of biocompatible polyurethane and polyurea nanoparticles based on polyoxyethylene castor oil derivative surfactant formed from O/W nano-emulsions by polymerization at the droplet interfaces in systems composed by aqueous solution/Kolliphor® ELP/medium chain triglyceride suitable for intravenous administration. Initial nano-emulsions incorporating highly hydrophilic materials were prepared by the phase inversion composition (PIC) method. After polymerization, nanoparticles with a small particle diameter (25–55 nm) and low polydispersity index were obtained. Parameters such as concentration of monomer, O/S weight ratio as well as the polymerization temperature were crucial to achieve a correct formation of these nanoparticles. Moreover, FT-IR studies showed the full conversion of the monomer to polyurethane and polyurea polymers. Likewise the involvement of the surfactant in the polymerization process through their nucleophilic groups to form the polymeric matrix was demonstrated. This could mean a first step in the development of biocompatible systems formulated with polyoxyethylene castor oil derivative surfactants. In addition, haemolysis and cell viability assays evidenced the good biocompatibility of KELP polyurethane and polyurea nanoparticles thus indicating the potential of these nanosystems as promising drug carriers.