Manganese enhanced MRI (MEMRI) offers many possibilities such as tract tracing and functional imaging in vivo. Mn is however neurotoxic and may induce symptoms similar to those associated with Parkinson's disease (manganism). The mechanisms of Mn-induced neurotoxicity are not clear. In this study, we combine synchrotron X-ray fluorescence microprobe (SR-XRF) and MEMRI techniques to investigate spatial distribution of Mn within the rat hippocampus and how Mn interacts with Ca, Fe and Zn at a cellular level. Images were acquired in the rat hippocampus (n=23) and using two injection routes: intra-cerebral (MnCl(2): 50mM, 10μL) and intra-peritoneal (MnCl(2): 100mM, 30mg/kg). For both injection routes, Mn is found in dentate gyrus and in CA3: control: 2.5±1.6, intra-peritoneal: 5.0±2.4, and intra-cerebral: 25.1±9.2μg/g. Mn follows Zn distribution and has a negative impact on the total amount of Zn and Fe. The Mn-enhanced MRI contrast is well correlated with the total Mn amount measured with SR-XRF (R(2)=0.93; p<0.002). After intra-cerebral injection, the hippocampal fissure is found to accumulate a large amount of Mn and yields a hypointense MRI signal, which may be ascribed to a reduction in T2. This study shows that SR-XRF is well suited to investigate Mn distribution at a mesoscale and that MRI is sensitive to low Mn concentrations. As perturbations in metal homeostasis may alter brain function, the injected dose of Mn in MEMRI studies needs to be carefully adjusted to obtain reliable functional information.