The geometric and hemodynamic characteristics of the left and right vertebral arteries (LVA, RVA) of six healthy volunteers were investigated for the supine (S) and the prone position (P) a common sleeping posture with head rotation. MRI images were used to reconstruct the subject specific three-dimensional solid models of the LVA and RVA from the level of the carotid bifurcation to the vertebrobasilar junction (VJ). Geometric parameters such as cross sectional area ratio, curvature, tortuosity and branch angle were estimated. MR-PCA was used to obtain the blood flow waveforms for the two positions and computational fluid dynamics (CFD) were used to assess the flow field in terms of wall shear stress (WSS) relative residence times (RRT) and localized normalized helicity (LNH). Significant geometric changes but moderate flow changes were observed for both vertebral arteries with head rotation. The CFD results at the VJ show that head rotation causes changes in the WSS distribution, RRT and LNH. Further studies are warranted to assess the clinical significance of the results in terms of atherosclerosis development at the VJ and how the observed geometric changes may affect blood flow to the brain in healthy subjects and vertebral artery stenosis patients, and in terms of increased rapture susceptibility in vertebrobasilar aneurysm patients.