Synovium-derived mesenchymal stromal cells (SM-MSCs) from seven Thoroughbreds with naturally occurring intra-articular fracture proliferated to over ten million cells by the second passage. Using three experimental Thoroughbreds, columnar osteochondral defects were made arthroscopically at the bilateral distal radius. Five million allogenic SM-MSCs were implanted into the right defect, and another five million were injected into the right radio-carpal joint (implantation site). No SM-MSCs were implanted into the left defect or the same joint (control site). At 3 and 6 weeks after surgery, ten million autologous SM-MSCs were injected into the right joints. Radiolucent volumes of defects calculated by analysis of postmortem CT images 9 weeks after surgery were decreased in implanted sites compared with control sites in all horses. The average scores for ICRS gross and histopathological grading scales in implanted sites were equal to or higher than those of the controls. These results suggest that allogenic implantation and subsequent autologous injection of SM-MSCs might not obstruct subchondral bone formation in defects.