Objective To identify the osteogenesis genes whose expression is altered in hypertrophic chondrocytes treated with H2O2. Methods Murine chondrogenitor cells (ATDC5) were differentiated into hypertrophic chondrocytes by Insulin-Transferrin-Selenium (ITS) treatment, and then treated with H2O2. Suitable conditions (concentration, time) were determined by using the MTT assay. After total RNA isolation and cDNA synthesis, the levels of 84 genes were determined using the PCR array, whereas quantitative RT-PCR was carried out to validate the PCR array data. Result We identified 9 up-regulated genes and 12 down-regulated genes, encoding proteins with various functions, such as collagen proteins, transcription factors, proteins involved in skeletal development and bone mineral metabolism, as well as cell adhesion molecules. Quantitative RT-PCR confirmed the altered expression of 5 down-regulated genes (Smad2, Smad4, transforming growth factor $\beta$ receptor 1, transforming growth factor $\beta$ receptor 3, and matrix metalloproteinase 10). Conclusions H2O2 significantly changed the expression of several genes involved in a variety of biological functions. Because of the link between oxidative damage and Kashin-Beck disease, these genes may also be involved in the deep-zone necrosis of the cartilage observed in Kashin-Beck disease.