We assessed the pathological changes of articular cartilage and subchondral bone on different locations of the knee after extracorporeal shockwave therapy (ESWT) in early osteoarthritis (OA). Rat knees under OA model by anterior cruciate ligament transaction (ACLT) and medial meniscectomy (MM) to induce OA changes. Among ESWT groups, ESWT were applied to medial (M) femur (F) and tibia (T) condyles was better than medial tibia condyle, medial femur condyle as well as medial and lateral (L) tibia condyles in gross osteoarthritic areas (p< 0.05), osteophyte formation and subchondral sclerotic bone (p< 0.05). Using sectional cartilage area, modified Mankin scoring system as well as thickness of calcified and un-calcified cartilage analysis, the results showed that articular cartilage damage was ameliorated and T+ F (M) group had the most protection as compared with other locations (p< 0.05). Detectable cartilage surface damage and proteoglycan loss were measured and T+ F (M) group showed the smallest lesion score among other groups (p< 0.05). Micro-CT revealed significantly improved in subchondral bone repair in all ESWT groups compared to OA group (p< 0.05). There were no significantly differences in bone remodeling after ESWT groups except F (M) group. In the immunohistochemical analysis, T+ F (M) group significant reduced TUNEL activity, promoted cartilage proliferation by observation of PCNA marker and reduced vascular invasion through observation of CD31 marker for angiogenesis compared to OA group (P< 0.001). Overall the data suggested that the order of the effective site of ESWT was T+ F (M)≧ T (M)> T (M+ L)> F (M) in OA rat knees.