Glial activation is thought to play a key role in pathogenesis of neurodegenerative disorders. Here we show that direct transplantation of bone marrow-derived mesenchymal stem cells (BM-MSC) results in alleviation of inflammatory responses associated with the cerebellum of Niemann-Pick disease Type C (NP-C) model mice. Immunohistochemical examinations using glial fibrillary acidic protein (GFAP) and F4/80 antibodies revealed that BM-MSC transplantation reduced significantly both of astrocytic and microglial activations in the cerebellum of NP-C mice. Expression of macrophage colony stimulating factor (M-CSF), a microglial activator, was also considerably down-regulated by the BM-MSC transplantation. These findings suggest that BM-MSC transplantation may have potential for a therapeutic role in the treatment of NP-C and other neurodegenerative brain disorders.