Proteomics approach to investigate protein changes in central nervous system (CNS) of mouse Experimental Autoimmune Encephalomyelitis (EAE) before and after treatment with mouse embryonic stem cell-derived neural precursor cells (ESC-NPs) in order to identify candidate mechanisms of damage in lesions of multiple sclerosis (MS). EAE induced by myelin oligodendrocyte glycoprotein. Intravenous injection of mouse ESC-NPs in EAE at score 3. Protein expression profiles in CNS between healthy, and clinical score 3 of EAE and treatment EAE were studied using two dimensional electrophoresis based proteomics approach coupled with MALDI TOF/TOF mass spectrometry. Clinical improvement was observed in EAE after the ESC treatment. Expression level of 30 proteins (out of 72 differentially expressed in EAE) were dramatically changed. The level of these 30 proteins was statistically under the differentiation border compare to the healthy control. Identified proteins supported the hypothesis that ESC help to decrease inflammation and increase remyelination in CNS of EAE. The exact function of these proteins and their involvement in the ESC-NPs treatment mechanism is under investigation.