Training has beneficial effects on the health of brain. The aim of this study was to evaluate the effect of resistance training with different intensities on serum levels of BDNF, Claudin11, and functional factors in MS patients. 30 women with MS (mean age 36. 1 ± 1. 8 years) were selected purposively, and were randomly divided into 3 groups: experimental 1 (resistance training with an intensity of 60% 1RM for 12 weeks, 3 sessions per week), experimental 2 (training with an intensity of 85% 1RM) and control (without regular training). Blood samples were collected in two steps (48 hours before the first training session and after the last training session). Results of the ELISA method and ANOVA with repeated measures showed that after 12 weeks, serum levels of BDNF in both experimental groups increased significantly compared with the pretest (P=0. 001). This increase was also significant in experimental 1 group compared with the control group (P=0. 002). Also, serum levels of Claudin11, muscle endurance and balance increased significantly in experimental groups in posttest compared with the pretest while fatigue decreased significantly (P=0. 001). These changes were significant in experimental groups compared with the control group. These findings showed that resistance training improves balance, fatigue and muscle endurance and increases levels of Claudin11 which is an important factor in the development of myelin sheath of nerve fibers. Also, an increase in BDNF levels which play a vital role in developing, maintaining and restoring nervous system was observed. In addition, in most cases, moderate intensity resistance training had an effect similar to high intensity training.