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Since introduction of autologous chondrocyte implantation (ACI), various factors have been described that influence the clinical outcome. The present paper investigates the influence of bone marrow edema at time of treatment on clinical function before and in the early clinical course after ACI.67 patients treated with ACI for cartilage defects of the knee joint were included. Presence of subchondral bone marrow edema was graded as absent (1), mild (2), moderate (3) or severe (4) using magnetic resonance (MR) imaging before surgery. All patients were assessed in terms of clinical function before surgery and 6 as well as 12 months after ACI using IKDC and Lysholm scores. Presence of subchondral edema was correlated with functional outcome.In 18 patients edema on initial MRI was graded as “absent”, while 17 patients had grade 2 edema, 19 patients had grade 3 edema and 13 patients had grade 4 edema. IKDC score increased significantly from 49.8 points (SD ± 14.9) to 72.3 points (SD ± 17.5) at 12 months (p < 0.01). At all time points investigated, patients of group “4” showed inferior results to all other groups (p < 0.05). In addition, in patients without any edema, better clinical function was detected compared to all other groups before surgery (p < 0.05) and compared to group 3 at 6 months following ACI (p < 0.05).Presence of severe subchondral bone marrow edema seems to correlate with knee function in patients with cartilage defects and may be a reliable prognostic factor for the early clinical course after ACI.