Purpose: The aim of this study was to determine the short term effects of two different exercise programs on muscle strength, normal range of motion, flexibility and the long term effects on functional level a during one-year follow-up period in amyotrophic lateral sclerosis (ALS) patients. Material and Methods: Twenty-six ambulatory ALS patients were included in the study. Following the first evaluation, subjects were assigned into two groups; supervised exercise group and home program group. Supervised program including breathing exercises, proprioceptive neuromuscular facilitation techniques, stretching exercises and functional mobility training which was applied 3 days in a week for 8 weeks. Home program consisted of breathing exercises, active/active-assisted range of motion and stretching exercises. Both groups were evaluated before the exercise programs in regards to joint range of motion, muscle shortness, muscle strength and functional activity level. The evaluations were repeated at the fourth and eighth weeks. Functional level of the subjects was followed for a one-year period. Results: Supervised exercise programs caused short-lived but significant improvements on joint limitation, muscle shortness and strength (p<0.05). Functional capacity level was sustained better in supervised exercise group during the one year-period (p<0.05). The results showed that home programs may be effective in maintaining the joint mobility and preventing muscle shortness and contractures, but it has no effect in sustaining muscle strength and functional capacity level (p<0.05). Conclusion: We concluded that the recommendation of exercise programs under professional supervision is important to maintain functional capacity, in the management of ALS patients, especially in the initial phase of the disease and in patients who are able to ambulate.