Using well-established measurement techniques like transmission electron microscopy (TEM), dynamic light scattering (DLS), small and wide angle X-ray scattering (SAXS, WAXS), susceptometry, and magnetorelaxometry, the distribution of the physical and magnetic size (magnetic moments) and magnetic anisotropy of a variety of structurally different magnetic nanoparticle samples (MNPs) is analyzed and compared. A term which accounts for the presence of weak magnetic areas (WMAs) within the MNPs was introduced to the widespread analysis model for M(H) data, enabling a consistent interpretation of the data in most of the systems. A comparison of the size distributions as obtained for the physical and the magnetic diameter suggests a multidomain structure for three single core systems under investigation, in all probability evoked by the presence of a wustite phase, as identified by WAXS. Analyzing the relationship d < dm < dc between the average single core diameter d, the effective magnetic (domain) size dm and the cluster diameter dc quantitatively, two qualitatively different magnetic structures in multicore MNP (MCMNP) systems were identified: (i) The magnetic moments of single cores within the MCMNP of fluidMAG tend to build flux closure structures, driven by dipole–dipole interaction. (ii) The magnetic behavior of Resovist® was attributed to the presence of domain sizes of about 12 nm within MCMNP, exceeding the single core diameters of 5 nm. Thereby, WAXS revealed a bimodal crystallite size distribution suggesting a crystallite merging process within the MCMNP. The value of the effective magnetic moment of these MCMNP could be explained within the presented “random moment cluster model” (RMCM). We conclude that the combination of physical and magnetic structure parameters obtained from complementary measurement methods allows a reliable assessment of the magnetic structure of single and multicore MNPs.