Background: Low endothelial shear stress (ESS) is associated with coronary plaque progression and high-risk plaque features. Coronary ESS profiling requires the three-dimensional luminal geometry and Computational Fluid Dynamic (CFD) assumptions to successfully model coronary blood flow. Hypothesis: To examine whether two typical CFD modeling assumptions, namely the exclusion of side branches and the blood model used, alter the determination of those arterial regions that are exposed to low ESS. Methods: Five excised human hearts were imaged with 64-detector row CT. Coronary arteries >1 mm in diameter were segmented and the coronary tree lumen was reconstructed with and without side branches. ESS was calculated for 3 models: a) the entire tree and a non-Newtonian blood model (reference standard) b) the entire tree and a Newtonian blood model and c) major coronaries only (no side branches) and a non-Newtonian blood model (Fig panel A). ESS was compared in each major coronary artery amongst models using Pearson’s correlation and via sensitivity and specificity to detect those 3 mm sections in the coronary circulation that contained the 10% of endoluminal surface with lowest ESS values. For sensitivity and specificity the first model (a) was considered the reference standard. Results: The Newtonian assumption for blood induced minimal change in ESS pattern other than a relative scaling of values. The exclusion of side branches however induced large, coronary-segment specific non-linear changes in both pattern and value. With no side branches, sensitivity and specificity to identify low ESS regions were 78% and 88%. With Newtonian blood and side branches, sensitivity and specificity were 89% and 98% (Fig panel B). Conclusion: Side branches are important for identifying areas of low ESS while the assumption that blood model behaves as a Newtonian fluid has negligible effect.