Abstract: Objective To study the expression of mitochondrial -Synuclein ( -SYN) in different rat brain regions and its effect on complex I activity of respiratory chain. Methods Immunoblot analysis was used to examine the expression level of mitochondrial -SYN in different brain regions and the transportation of -SYN into isolated mitochondria. The mitochondrial complex I activity of respiratory chain was measured by measuring the change of NADH maximal absorbance at 340 nm. Results -SYN was found to localize in mitochondria throughout the rat brain, with the amount being varied in different brain regions. Incubation of recombinant -SYN protein with isolated mitochondria led to transportation of this protein into mitochondria. Incubation of -SYN protein with isolated mitochondria decreased the complex I activity of respiratory chain in a dose-dependent manner. Conclusion The amount of mitochondrial -SYN is varied in different brain regions. Mitochondrial -SYN may come from the transportation of cytoplasmic -SYN and may regulate the complex I activity of respiratory chain.