We report about a combined structural and magnetometric characterization of self-assembled magnetic nanoparticle arrays. Monodisperse iron oxide nanoparticles with a diameter of 20nm were synthesized by thermal decomposition. The nanoparticle suspension was spin-coated on Si substrates to achieve self-organized arrays of particles and subsequently annealed at various conditions. The samples were characterized by x-ray diffraction, and bright and dark field high resolution transmission electron microscopy. The structural analysis is compared to magnetization measurements obtained by superconducting quantum interference device magnetometry. We can identify either multi-phase FexO/γ-Fe2O3 or multi-phase Fe xO/Fe3O4 nanoparticles. The Fe xO/γ-Fe2O3 system shows a pronounced exchange bias effect which explains the peculiar magnetization data found for this system. © 2011 IOP Publishing Ltd.