A 3.5 x 4 mm tubular osteochondral defect was created on the right medial femoral condyles of 51 adult rabbits. In the control group (CG), defects were left untreated. In the early-(ETG) and late-(LTG) treatment groups, defects were treated by an osteoperiosteal graft 1 and 12 weeks, respectively, after the index procedure. Synovial fluid (SF) samples were collected regularly and proteoglycan fragments (PF), total collagen (TC) and collagenase (MMP-1) levels were measured. Rabbits were killed at 4 (early period), 12 (intermediate period), or 24 (late period) weeks postoperatively. Histological examination indicated a more successful healing in both grafting groups than in the CG, but without any difference at any time period between the grafting groups. In the CG, PF, and TC levels in SF increased continuously until the late period, indicating an ongoing degenerative activity in the joints. In contrast, SF marker levels in both grafting groups indicated that normalization in joint metabolism could be achieved-at least partially-after treatment. However, PF levels in the SF showed that the treatment of defects in earlier stages might result in better outcomes since the negative effects were more prominent in chronic stages, presumably due to the more prolonged period of disturbed homeostasis. Thus, histological values and SF marker levels indicated that treatment of osteochondral defects at any time of the disease had a positive effect on healing when compared to no treatment. Early treatment might better assist the recovery of joint homeostasis than late treatment.