A double hydrophilic block copolymer was synthesized by controlled free radical polymerization, namely by the RAFT method, from a poly(ethylene oxide) macromonomer and a cationic acrylate. Stoichiometric complexes with sodium decanoate and with sodium perfluorodecanoate were prepared by self-assembly. Both complexes are soluble in water forming core-shell nanoparticles with hydrodynamic radii of 54 and 22 nm, respectively, and neutral zeta potentials. The complex containing decanoate decomposed upon dilution, while the complex with perfluorodecanoate is stable even against dialysis and in salt solution. Only the nanoparticles containing perfluorodecanoate show a strong contrast in small-angle X-ray scattering (SAXS). It is produced from their cores that have an elliptical shape (short axes = 8.5 nm, long axis = 23.3 nm) and a sharp density transition to the shell. The cores exhibit an internal lamellar structure with a long period of 3.65 nm consisting of fluorocarbon rich lamellae (d(1) = 3.00 nm) and lamellae enriched in ionic groups (d(2) = 0.65 nm). These fluorinated nanoparticles coexist in physiological buffer with human serum albumin and fibrinogen without inducing aggregation. Moreover, the content of alpha-helix of these serum proteins increased when in solution with the fluorinated nanoparticles.