(1) The study’s objective is to assess sinus hemodynamics differences between stenotic native bicuspid aortic valve (BAV) and native tricuspid aortic valve (TrAV) sinuses in order to assess sinus flow shear and vorticity dynamics in these common pathological states of the aortic valve. (2) Representative patient-specific aortic roots with BAV and TrAV were selected, segmented, and 3D printed. The flow dynamics within the sinus were assessed in-vitro using particle image velocimetry in a left heart simulator at physiological pressure and flow conditions. Hemodynamic data calculations, vortex tracking, shear stress probability density functions and sinus washout calculations based on Lagrangian particle tracking were performed. (3) (a) At peak systole, velocity and vorticity in BAV reach 0.67 ± 0.02 m/s and 374 ± 5 s−1 versus 0.49 ± 0.03 m/s and 293 ± 3 s−1 in TrAV; (b) Aortic sinus vortex is slower to form but conserved in BAV sinus; (c) BAV shear stresses exceed those of TrAV (1.05 Pa versus 0.8 Pa); (d) Complete TrAV washout was achieved after 1.5 cycles while it was not for BAV. 4) In conclusion, sinus hemodynamics dependence on the different native aortic valve types and sinus morphologies was clearly highlighted in this study.