Pilates is an exercise method which increases strength and endurance of core muscles and improves flexibility, dynamic postural control and balance. This study aimed to analyze and compare the effects of Mat and Reformer Pilates methods in Patients with Multiple Sclerosis (MS). 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. 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.