The advent of microelectromechanical systems (MEMS) sensors has enabled real-time wall shear stress (WSS) measurements with high spatial and temporal resolution in a 3-D bifurcation model. To optimize intravascular shear stress assessment, we evaluated the feasibility of catheter/coaxial wire-based MEMS sensors in the abdominal aorta of the New Zealand white (NZW) rabbits. Theoretical and computational fluid dynamics (CFD) analyses were performed. Fluoroscope and angiogram provided the geometry of aorta, and the Doppler ultrasound system provided the pulsatile flow velocity for the boundary conditions. The physical parameters governing the shear stress assessment in NZW rabbits included (1) the position and distance from which the MEMS sensors were mounted to the terminal end of coaxial wire or the entrance length, (L(e)), (2) diameter ratios of aorta to the coaxial wire (D(aorta) /D(coaxial wire)=1.5-9.5), and (3) the range of Reynolds numbers (116-1550). At an aortic diameter of 2.4mm and a maximum Reynolds number of 212 (a mean Reynolds number of 64.2), the time-averaged shear stress (tau(ave)) was computed to be 10.06 dyn cm(-2) with a systolic peak at 33.18 dyn cm(-2). In the presence of a coaxial wire (D(aorta)/D(coaxial wire)=6 and L(e)=1.18 cm), the tau(ave) value increased to 15.54 dyn cm(-2) with a systolic peak at 51.25 dyn cm(-2). Real-time intravascular shear stress assessment by the MEMS sensor revealed an tau(ave) value of 11.92 dyn cm(-2) with a systolic peak at 47.04 dyn cm(-2). The difference between CFD and experimental tau(ave) was 18.5%. These findings provided important insights into packaging the MEMS sensors to optimize in vivo shear stress assessment.