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The aim of this study was to investigate the effects of two exercise programs on lower extremity function in patients with juvenile idiopathic arthritis.Thirty patients with juvenile idiopathic arthritis participated in this study. Pain, passive range of motion, muscle strength, balance, and functional abilities were assessed with the Numeric Rating Scale, goniometer, handheld dynamometer, Flamingo Balance Test, Functional Reach Test, 10-meter walking test, 10-stair climbing test, and Childhood Health Assessment Questionnaire. Participants were randomly assigned to the strengthening exercise group (group 1, n = 15) or the proprioceptive-balance exercise group (group 2, n = 15).Intragroup analysis showed statistically significant improvements in all outcome measures except muscle strength in the hip and ankle after strengthening exercises in group 1. However, statistically significant improvements were found in all outcome measures after the proprioceptive-balance exercises in group 2. Intergroup analysis showed statistically significant improvement in all outcome measures in group 2 except for the Numeric Rating Scale, Childhood Health Assessment Questionnaire, and passive range of motion scores and hip extension and knee flexion muscle strengths.This study demonstrates that exercise treatment significantly improves musculoskeletal symptoms in patients with juvenile idiopathic arthritis. However, balance-proprioceptive exercises prove to be effective more than strengthening exercises for improving lower extremity function such as walking, climbing stairs, and balance in patients with juvenile idiopathic arthritis.