Mesenchymal stem cells are widely used in the treatment of many diseases, including osteoarthritis, due to their ability to differentiate into cartilage. The high chondrogenic differentiation potential of synovial fluid-derived mesenchymal stem cells increases the importance of these cells in osteoarthritis treatments. Addition of BMP-9 and TGF-ß3 into chondrogenic differentiation medium, increases chondrogenic differentiation and they also cause hypertrophic effects on chondrocytes. In our study, it was aimed to demonstrate the effects of BMP-9 and TGF-ß3 on cell hypertrophy by adding them into the chondrogenic basal medium during in vitro chondrogenic differentiation. In the study, stem cells in passage 5 and chondrocytes in passage 1 were cultured in a transwell coculture system and six experimental groups were formed. Cell hypertrophy was demonstrated by examining MMP-13 and RUNX -2 gene expressions, in stem cells where chondrogenesis were induced in transwell coculture. Although the addition of BMP-9 and TGF-ß3 to the chondrogenic medium increased hypertrophic gene expressions in experimental groups compared to control, the results were not statistically significant. The addition of BMP-9 and TGF -ß3, separately or in combination, during the chondrogenic differentiation of stem cells does not cause significant chondrocyte hypertrophy.