The objective was to evaluate the functional performance over a 2-year period following autologous chondrocyte implantation (ACI) in an open knee procedure compared to microfracture. Objective functional outcome was studied as secondary analysis in a subgroup of patients, in a randomized clinical trial, with concealed allocation and independent evaluators. Sixty-seven patients with local cartilage defect, with a mean size of 2.4 cm(2) (SD 1.5) of the femoral condyle of the knee were included. Thirty-three patients underwent the microfracture and 34 the ACI procedure. An identical rehabilitation protocol was implemented for both groups. Active knee flexion and extension range, anterior laxity, knee extension strength (concentric at 60 degrees /s) and single leg hop performance (single hop, crossover triple hop and 6 m timed hop test) were evaluated pre-surgery and at 6, 9,12 and 24 months post-surgery. We calculated the symmetry index for individual and four performance tests pooled. Mixed linear model analyses were used with confidence interval set at 95%. The change over 2 years for the pooled performance-based tests was comparable between the two treatment arms. At 2 years, 70% (38/54) of all patients returned to >85% symmetry in overall functional performance. A decrease in functional performance at 6 months following ACI resulted in slower recovery at 9 and 12 months compared to microfracture. Rehabilitation following both cartilage repair procedures is a lengthy process. At 2 years after surgery, ACI patients have similar overall functional outcome compared to microfracture patients.