Catheters are used to measure translesional pressure gradients in the stenosed coronary arteries. Uses of catheters during coronary angioplasty cause flow obstructions. A narrowed flow cross section with catheter effectively introduced a tighter stenosis than the enlarged residual stenoses after balloon angiplasty. Catheters in blood vessels cause pressure gradient rise and blood flow drop during the measurements. In this study, three dimensional computer simulations are conducted to investigate the flow blockage effects due to the catheter obstructions during the coronary angioplasty. The computer simulation models are generated by the data, which are measured by coronary angiogram, and the blood is treated as non-Newtonian fluid. The velocity, pressure, and wall shear stress variations are observed for the estimate of damages of blood vessel. This study is also extended to investigate the effects of stenotic vessel size, and shape and catheter size and location.