Graft hypertrophy is a major complication in the treatment for localized cartilage defects with autologous chondrocyte implantation (ACI) using periosteal flap and its further development, Novocart (a matrix-based ACI procedure). The aim of the present study is to investigate individual criteria for the development of graft hypertrophy by NOVOCART 3D implantation of the knee in the post-operative course of 2 years. Forty-one consecutive patients with 44 isolated cartilage defects of the knee were treated with NOVOCART 3D implants. Individual criteria and defect-associated criteria were collected. Follow-up MRIs were performed at 3, 6, 12 and 24 months. The NOVOCART 3D implants were measured and classified. The modified MOCART Score was used to evaluate quality and integration of the NOVOCART 3D implants in MRI. Graft hypertrophy was observed in a total of 11 patients at all post-operative time points. We were able to show that NOVOCART 3D implantation of cartilage defects after acute trauma and osteochondritis dissecans (OCD) led to a significantly increased proportion of graft hypertrophy. No other individual criteria (age, gender, BMI) or defect-associated criteria (concomitant surgery, second-line treatment, defect size, fixation technique) showed any influence on the development of graft hypertrophy. The modified MOCART Score results revealed a significant post-operative improvement within 2 years. The aetiology of cartilage defects appears to have a relevant influence for the development of graft hypertrophy. Patients, who were treated with NOVOCART 3D implants after an acute event (acute trauma or OCD), are especially at risk for developing a graft hypertrophy in the post-operative course of two years. Case series, Level IV.