BACKGROUND: Pilates is an exercise method which increases strength and endurance of core muscles and improves flexibility, dynamic postural control and balance. OBJECTIVE: To analyze and compare the effects of Mat and Reformer Pilates methods in Patients with Multiple Sclerosis (MS). METHODS: Thirty-eight patients with MS were included in the study. Participants were randomly divided into 3 groups as Mat Pilates, Reformer Pilates and control groups. The subjects in the Pilates groups did Mat or Reformer Pilates for 8 weeks, 2 days a week. The control group did breathing and relaxation exercises at home. Balance, functional mobility, core stability, fatigue severity and quality of life were evaluated. RESULTS: Balance, functional mobility, core stability, fatigue severity and quality of life improved after Pilates in Mat and Reformer Pilates groups (p < 0.05). On the other hand, we could not find any changing in the control group (p > 0.05). When the gain obtained in the Pilates groups is compared, it has been observed that progress has been more in trunk flexor muscle strength in the Reformer Pilates group (p < 0.05) and that the gain has been similar in the other parameters (p > 0.05). CONCLUSIONS: As a result, patients with MS have seen similar benefits in Reformer Pilates and Mat Pilates methods.