The objective of this study is screening the shear stress related proteins in chondrocytes using twodimensional electrophresis and MALDI-TOF. C-28/I2 cell line were grown. The fluid-induced shear stress(FISS) was applied using a cone viscometer at a rotational velocity of 80rpm for periods of 12 hours. Control cultures were tested under identical conditions without mechanical load application. Collected samples were used for the two-dimensional electrophoresis and MALDI-TOF. The identified proteins were calcyclin, RPE-spondin, interleukin-2, extracellular signal regulated kinase (ERK), lamin B2, porA protein, and RET-ELE1 protein. All of them showed a decreased expression. In conclusion, seven proteins were identified as a shear stress related proteins in chondrocytes. As the destruction of articular cartilage is one of main pathogenesis of TMJ internal derangement, this study will give useful information for the understanding of the molecular aspect of TMJ disease.