Iron oxide nanoparticles (ION) provide high sensitivity for MRI cell tracking, but signal reductions cannot easily be separated from those originating from endogenous iron. We combine 57Fe-ION MRI with laser ablation-inductively coupled plasma-mass spectrometry for differentiation between endogenous iron (56Fe) and applied ION. We establish 57Fe-ION as contrast agent and assess their long-term fate. The technique facilitates specific and quantifiable cell tracking. ION were first internalized by phagocyting cells predominantly in liver and spleen, but in the long-term relocated to endogenous iron sources as the blood or red pulp of the spleen and, interestingly, also in the brain parenchyma.