Transition metals have been suggested to play a pivotal role in the pathogenesis of Parkinson's disease (PD). X-ray microscopy combined with a cryogenic setup is a powerful method for elemental imaging in low concentrations and high resolution in intact cells, eliminating the need for fixation and sectioning of the specimen. Here, we performed an elemental distribution analysis in cultured primary midbrain neurons with a step size in the order of 300 nm and ~0.1 ppm sensitivity under cryo-conditions by using X-ray fluorescence (XRF) microscopy. We report the elemental mappings on the sub-cellular level in primary mouse dopaminergic (DAergic) and non-DAergic neurons after treatment with transition metals. Application of Fe(2+) resulted in largely extracellular accumulation of iron without preference for the neuronal transmitter subtype. A quantification of different Fe oxidation states was performed using XANES analysis. After treatment with Mn(2+) a cytoplasmic/paranuclear localization of Mn was observed preferentially in DAergic neurons, while no prominent signal was detectable after Mn(3+) treatment. Immunocytochemical analysis correlated the preferential Mn uptake to increased expression of voltage-gated calcium channels (VGCC) in DAergic neurons. We discuss the implications of this differential elemental distribution for the selective vulnerability of DAergic neurons and PD pathogenesis. © 2012 International Society for Neurochemistry, J. Neurochem. (2012) 10.1111/jnc.12073.