We report about a combined structural and magnetometric characterization of self-assembled magnetic nanoparticle arrays. Monodisperse iron oxide nanoparticles with a diameter of 20 nm 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, bright and dark field high resolution transmission electron microscopy (HRTEM). The structural analysis is compared to the magnetic behavior investigated by superconducting interference device (SQUID) magnetometry. We can identify either multi-phase FeO/g-Fe2O3 or multi-phase FeO/Fe3O4 nanoparticles. The FeO/g-Fe2O3 system shows a pronounced exchange bias effect which explains the peculiar magnetization data obtained for this system.