The magnetic response of nanometer sized Co nanoparticles (NP) prepared using reverse micelle solutions are presented. The use of complementary structural and morphological probes (like transmission electron microscopy, high resolution electron microscopy, X-ray absorption spectroscopy) allowed to relate the magnetic properties to the size, morphology, composition and atomic structure of the nanoparticles. All data agree on the presence of a core–shell structure of NPs made of a metallic Co core surrounded by a thin Co-oxide layer. The core–shell microstructure of NPs affects its magnetic response mainly raising the anisotropy constant.