The purpose of this study was to analyze normal and pathological MR findings in osteochondral autograft transfer systems (OATS) of the knee and ankle in the longitudinal follow-up and in relation to the clinical findings. MR imaging was performed in 55 patients (21 females: 34 males; mean age 34.5+/-12.1 years) after OATS procedures in the knee (n=45) and ankle (n=10). MR sequences were obtained with and without intravenous Gd-DTPA administration within the first year post-operatively, in 30 patients within the second and in 13 patients in the third year. One hundred and five OATS cylinders were implanted. MR findings consistent with osteonecroses were detected in eight cylinders (n=6 in the knee and n=2 in the ankle) in six patients; four out of eight were demonstrated during the first year and four/eight in the second year. Edema around and/or in the cylinders was found in 28/55 of the patients within the first year, five/30 in the second year and in two/13 in the third year. No substantial changes in the cartilage signal intensity or the cartilage-cartilage interface were demonstrated in the longitudinal follow-up within the first three years. Clinical and MR findings were not consistently associated in particular in the patients with osteochondral autograft necroses.