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Background Femoropopliteal bypass is a common vascular reconstructive procedure. A significant proportion of bypasses become ineffective within 1 year because of occlusion due to progression of intimal hyperplasia (IH). Methods The clinical part of the study involved an analysis of 43 patients with proximal femoropopliteal bypass, which became occluded no later than 1 year from the procedure, who were successfully treated with thrombolysis. Morphological changes of intima in the anastomosis (evaluated angiographically) and the angle of the distal end-to-side anastomosis were evaluated. In the second part of the study, blood flow in the distal end-to-side anastomosis was modeled experimentally (by particle image velocimetry) and numerically (by computational fluid dynamics). The results were correlated with the previously identified locations of IH. Results We proved that the locations of IH correlate with the locations of disturbed blood flow, increased wall shear stress, and stagnation points as documented by experimental visualization and angiographic findings. We also confirmed that anastomoses with more acute angles are less prone to IH and occlusion of the lumen. Conclusion We suggest that a better understanding of the hemodynamics and its influence on IH should lead to an optimized graft design by adopting a more acute angle of the anastomosis.