Stem cells therapy is considered to be a very promising route for treating neurological disorders of the CNS. Two main therapeutic strategies exist: in the first, stem-cells are transplanted with the intent of replacing dying tissue and integrating to the neuronal network; the second strategy involves transplantation of stem-cells which deliver trophic factors that regulate, maintain and prevent further tissue deterioration. One of the main issues in stem cells therapy is determining their fate in the host tissue after transplantation, and moreover, evaluating their migration and homing capabilities towards impaired tissue. Here, we demonstrated with cellular MRI that mesenchymal stem cells pre-labeled with magnetic nanoparticles can migrate to Quinolinic acid induced lesion - a known model of Huntington disease (HD). Such treatments are now being pursued in experimental model of Parkinson's disease (PD). There, we have been able to delineate transplanted stem-cells, labeled with super-paramagnetic-iron-oxide (SPIO) paricles, from brain tissue and follow their migration patterns in-vivo in the Quinolinc acid (QA) animal model for HD. We are currently employing the 6-OHDA and MPTP animal models for PD to induce inflammatory or apoptotic cell death, respectively, and study migration patterns of the transplanted stem-cells in the different types of neuronal damage.