In earlier work, it was demonstrated that the flow in models of the vertebro-basilar junction is highly three-dimensional and the geometry exerts a strong influence on the hemodynamics. The morphology of the vertebro-basilar junction is very variable amongst individuals. In a study of 85 human vertebro-basilar junctions, the angle between the vertebral arteries varied between 10 and 160 degrees. To determine how the flow is influenced by this geometrical parameter, the flow is studied both experimentally, with laser Doppler velocimetry, and numerically, with a finite element package. A series of junction models is used with a range of confluence angles (45, 85 and 125 degrees). It appears that the angle of confluence has a strong influence on the structure and strength of the secondary flow field. The secondary velocities persist far downstream. Furthermore, near the apex, a region with low velocities is present. The larger the confluence angle is, the larger this region is, and even backflow may occur. In addition, the occurrence of atherosclerotic plaques in 85 human vertebro-basilar junctions is studied. Only one preferential location was found: the apex, the other plaques seem to be randomly distributed. The magnitude of the confluence angle of junctions with sharp-edged apices has a significant influence (p = 0.006) on the occurrence of a plaque at the apex. Apparently, a large confluence angle is a geometrical risk factor for atherosclerosis.