This study was performed to investigate the expressions of the SOX trio, PTHrP (parathyroid hormone-related peptide) and IHH (Indian hedgehog protein) in OA (osteoarthritis) using surgically induced rat OA model. After 12 weeks, the articular cartilage from the distal femur was harvested. The expressions of the SOX trio, PTHrP and IHH were explored at gene, protein and epigenetic levels by real-time PCR (n=5), immunohistochemistry (n=5) and MSP (methylation-specific PCR). The findings from OA cartilage of the right knees were compared with those from the left knees as the control. The gene expressions of SOX-5, −6, −9 decreased by 58, 20 and 40%, respectively, in the OA cartilage, while their respective protein expressions increased. The PTHrP and IHH gene expressions decreased by 75 and 81%, respectively, although their protein expressions increased. Findings from MSP demonstrated increased methylation in the promoter regions of SOX-5 and −9 genes. This study demonstrated that increased methylation in the promoters of these genes may explain the low gene expression in the surgically induced OA model, whereas elevated protein expression is speculated to be from lag effect in the gene—protein expression.