Iron oxide nanoparticles with diameters of 20.1 and 8.5 nm coated with phospholipids containing poly-(ethylene glycol) (PEG) tails were studied using small-angle X-ray scattering (SAXS), transmission electron microscopy, dynamic light scattering, and magnetometry. Novel SAXS data analysis methods are applied to build three-dimensional structural models of the nanoparticles coated with PEGylated phospholipids in aqueous solution. The SAXS data demonstrate that the density inside iron oxide nanoparticles is not uniform and depends on the nanoparticle size, which in turn is dependent on the reaction conditions. This heterogeneity is attributed to the presence of two crystalline phases, spinel and wüstite, in the nanoparticles. Because of magnetic properties, the nanoparticles in solution associate in flexible dynamic clusters consisting on average of four individual cores. The magnetometry further supports the SAXS-based models.