Objective:To investigate the effect of repetitive transcranial magnetic stimulation(rTMS)on dopaminergic neurons and brain-derived neurotrophic factor(BDNF) in the substantia nigra (SN) of mouse with Parkinson’s disease (PD ), and to disclose the possible mechanisms. Methods: Thirty-two male C57BL/6J mice were equally randomized into normal saline (NS), sham-rTMS (s-rTMS), PD model and rTMS groups. PD model was established with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) in mice. The animals in rTMS group received 5 trains of 1 pulse/s for 25 s, at an intensity of 1 Tesla (T) daily for 2 weeks. After the treatment of rTMS, the changes in expression of tyrosinehy droxylase (TH) and BDNF in the SN of animals were observed by immunohistochemical technique; the quantitative analysis was performed by image analysis system. Results: Compared with NS group, the numbers of TH and BDNF immunoreactive(TH-ir and BDNF-ir)cells and the corrected optical density (CD) values in PD and s-rTMS group were significantly lower than those in the NS group (all P<0.01); the numbers in rTMS group were significantly higher compared with those in the PD and s-rTMS groups (all P<0.05); and the numbers were not significantly different between the s-rTMS and PD groups(P>0.05). Correlation analysis showed a positive correlation between the count of TH-ir and BDNF-ir cells (r=0.949, P<0.01); and positive correlation was also noted between the CD values of TH-ir and BDNF-ir cells (r=0.880, P<0.01).Conclusion: It is suggested that rTMS has protective effects on dopaminergic neurons in the SN of PD mice, and the mechanism might be related to the up-regulation of BDNF expression.