This paper describes a polymer-based shear stress sensor built on catheter for in vivo measurements and potential application in atherosclerosis diagnosis. MEMS shear stress sensor with backside wire bonding has been used to address in vitro applications for micro-scale hemodynamics with high temporal and spatial resolution. However, to assess shear stress in the tortuous and dynamic arterial circulation, we had to develop a new generation of polymer- and catheter-based sensors that are both flexible and deployable. The individual sensor was packaged near the tip of a catheter for intravascular shear stress analysis. The wire bonding and electrode leads were insulated by a film of Parylene C and were connected to the external circuit along the guide-wire. The sensor was deployed through the catheter into the aorta of New Zealand White (NZW) rabbits by the femoral cut-down procedure. Based on the heat transfer principle, the device was able to detect small temperature perturbation in response to the pulsatile flow at ̃ 200 beats/minutes in the rabbits. The sensor was calibrated in the presence of rabbit blood flow at 37.8°C. We demonstrated the feasibility of translating a polymer- based device for dynamic intravascular measurement with a potential for clinical applications in detecting coronary artery disease and stroke.