MRI-based quantification of dopaminergic neurons (DN) and their neuromelanin (NM) in substantia nigra (SN) has great potential to serve as a specific biomarker for neurodegeneration in movement disorders. We used 22-µm-resolution post mortem MR microscopy combined with ion beam microscopy to characterize the magnetic properties of DN. MR microscopy visualized individual DN and provided 3D cellular maps of the entire SN. Static dephasing was determined as main effective transverse relaxation mechanism of DN. We characterized the susceptibility of iron in DN and estimated that the contribution of DN to R2* and QSM may also be detected with in vivo MRI.