There is a spatial disposition to atherosclerosis along the aorta corresponding to regions of flow disturbances. The objective of the present study is to investigate the detailed distribution of hemodynamic parameters (wall shear stress (WSS), spatial gradient of wall shear stress (WSSG), and oscillatory shear index (OSI)) in the entire length of C57BL/6 mouse aorta with all primary branches (from ascending aorta to common iliac bifurcation). The detailed geometrical parameters (e.g., diameter and length of the vessels) were obtained from casts of entire aorta and primary branches of mice. The flow velocity was measured at the inlet of ascending aorta using Doppler flowprobe in mice. The outlet pressure boundary condition was estimated based on scaling law. The continuity and Navier-Stokes equations were solved using three-dimensional finite element method (FEM). The model prediction was tested by comparing the computed flow rate with the flow rate measured just before the common iliac bifurcation, and good agreement was found. It was also found that complex flow patterns occur at bifurcations between main trunk and branches. The major branches of terminal aorta, with the highest proportion of atherosclerosis, have the lowest WSS, and the relatively atherosclerotic-prone aortic arch has much more complex WSS distribution and higher OSI value than other sites. The low WSS coincides with the high OSI, which approximately obeys a power law relationship. Furthermore, the scaling law between flow and diameter holds in the entire aorta and primary branches of mice under pulsatile blood flow conditions. This model will eventually serve to elucidate the causal relation between hemodynamic patterns and atherogenesis in KO mice.