Collagen II and aggrecan are the major components of the cartilage extracellular matrix (ECM) that determine the structure and function of the hyaline articular cartilage. Therefore, their examination should be included in the evaluation of the repair tissue, which is formatted into osteochondral defects (ODs). In this study, the effect of allogeneic-derived stem cells (DSCs), including bone marrow-DSCs (BMDSCs), adipose-DSCs (ADSCs), and synovial membrane-DSCs (SMDSCs), implantation on collagen II and aggrecan production was evaluated. Forty-eight New Zealand rabbits underwent the creation of 3×3mm sized ODs in the femoral patellar groove on both knees and were then randomly assigned to three groups. In all groups, the ODs in the right limbs were filled with fibrin glue (FG), whereas the ODs in the left limbs were filled with ADSCs+FG in group A, with BMDSCs+FG in group B and with SMDSCs+FG in group C. After 12 weeks the repair tissues were immunohistologically assessed for collagen II and aggrecan. Accordingly, FG and ADCSs (p=0.003), BMDSCs (p=0.017), and SMDSCs (p=0.003) implantation resulted in significantly stronger expression of collagen II in the reparative tissue compared with the FG groups. Also, the newly formed tissue in the BMDSCs+FG (p=0.015) and SMDSCs+FG (p=0.003) groups expressed significantly higher aggrecan compared with the FG groups, whereas BMDSCs+FG (p=0.030) and SMDSCs+FG (p=0.002) transplantation promoted significantly higher aggrecan composition compared with ADSCs+FG. These findings indicate the profound impact of BMDSCs and SMDSCs on the ECM quality of the repair tissue. Additionally, the inefficiency of FG to induce a well-developed ECM in the repair area was highlighted.