Manganese (Mn) is known to pass across the blood–brain barrier and interact with dopaminergic neurons. However, the knowledge on the subcellular distribution of Mn in these cell types upon exposure to Mn remained incomplete. This study was designed to investigate the subcellular distribution of Mn in blood–brain barrier endothelial RBE4 cells, blood–cerebrospinal fluid barrier choroidal epithelial Z310 cells, mesencephalic dopaminergic neuronal N27 cells, and pheochromocytoma dopaminergic PC12 cells. The cells were incubated with 100 μM MnCl 2 with radioactive tracer 54Mn in the culture media for 24 h. The subcellular organelles, i.e., nuclei, mitochondria, microsomes, and cytoplasm, were isolated by centrifugation and verified for their authenticity by determining the markers specific to cellular organelles. Data indicated that maximum Mn accumulation was observed in PC12 cells, which was 2.8, 5.2- and 5.9-fold higher than that in N27, Z310 and RBE4 cells, respectively. Within cells, about 92%, 72%, and 52% of intracellular 54Mn were found to be present in nuclei of RBE4, Z310, and N27 cells, respectively. The recovery of 54Mn in nuclei and cytoplasm of PC12 cells were 27% and 69%, respectively. Surprisingly, less than 0.5% and 2.5% of cellular 54Mn was found in mitochondrial and microsomal fractions, respectively. This study suggests that the nuclei may serve as the primary pool for intracellular Mn; mitochondria and microsomes may play an insignificant role in Mn subcellular distribution.