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Objective Matrix-associated autologous chondrocyte implantation (ACI) and microfracture (MF) are well-established treatments for cartilage defects of the knee. However, high-level evidence comparing microfracture and spheroid technology ACI is limited.Design Prospective, phase III clinical trial with patients randomized to ACI (N= 52) or MF (N= 50). Level of evidence: 1, randomized controlled trial. Both procedures followed standard protocols. For ACI 10 to 70 spheroids/cm2were administered. Primary outcome measure was the Knee Injury and Osteoarthritis Outcome Score (KOOS). This report presents results for 36 months after treatment.Results Both ACI and MF showed significant improvement over the entire 3-year observation period. For the overall KOOS, noninferiority of ACI (the intended primary goal of the study) was formally confirmed; additionally, for the subscores “Activities of Daily Living” and “Sport and Recreation,” superiority of ACI over MF was shown at descriptive level. Occurrence of adverse events were not different between both treatments (ACI 77%; MF 74%). Four patients in the MF group required reoperation which was defined as treatment failure. No treatment failure was reported for the ACI group.Conclusions Patients treated with matrix-associated ACI with spheroid technology showed substantial improvement in various clinical outcomes after 36 months. The advantages of ACI compared with microfracture was underlined by demonstrating noninferiority, in overall KOOS and superiority in the KOOS subscores “Activities of Daily Living” and “Sport and Recreation.” In the present study, subgroups comparing different age groups and defect sizes showed comparable clinical outcomes.