Context: Patients with chronic ankle instability (CAI) have demonstrated atrophy of foot and ankle musculature and deficits in ankle strength. The effect of rehabilitation on muscle morphology and ankle strength has not previously been investigated in patients with CAI. Objective: Our objective was to analyze the effect of impairment-based rehabilitation on intrinsic and extrinsic foot and ankle muscle volumes and strength in patients with CAI. Design: Controlled laboratory study. Setting: Laboratory. Patients: Five young adults with CAI. Intervention: Twelve sessions of supervised impairment-based rehabilitation that included range of motion, strength, balance, and functional exercises. Main Outcome Measures: Measures of extrinsic and intrinsic foot muscle volume and ankle strength measured before and after 4 weeks of supervised rehabilitation. Novel fast-acquisition magnetic resonance imaging was used to scan from above the femoral condyles through the entire foot. The perimeter of each muscle was outlined on each axial slice and then the 2-dimensional area was multiplied by the slice thickness (5 mm) to calculate muscle volume. Plantar flexion, dorsiflexion, inversion, and eversion isometric strength were measured using a hand-held dynamometer. Results: Rehabilitation resulted in hypertrophy of all extrinsic foot muscles except for the flexor hallucis longus and peroneals. Large improvements were seen in inversion, eversion, and plantar flexion strength following rehabilitation. Effect sizes for significant differences following rehabilitation were all large and ranged from 1.54 to 3.35. No significant differences were identified for intrinsic foot muscle volumes. Conclusion: Preliminary results suggest that impairment-based rehabilitation for CAI can induce hypertrophy of extrinsic foot and ankle musculature with corresponding increases in ankle strength.