Bioprosthetic valve thrombosis has been considered uncommon, but recent studies have shown that it is more frequent than previously thought. Insufficient washout of the aortic sinus is believed to be a risk factor for bioprosthetic valve thrombosis. The objective of this in vitro experiment was to investigate the impact of aortic root morphology on blood flow in the aortic sinus and to relate these results to in vivo data obtained in patients with a transcatheter aortic valve implant. Two compliant aortic root phantoms with different morphologies (symmetrical and patient-specific) were fabricated with silicone. A bioprosthetic aortic valve was inserted in both phantoms. Haemodynamic measurements were performed in a pulsatile flow-loop replicating physiological flow and pressure conditions. The flow in the aortic root was visualized by injecting contrast agent (CA). The distribution of the CA was captured by a high-speed camera, and image post-processing was performed to quantify CA distribution in the aortic sinus. The results were compared with angiographic images after a transcatheter aortic valve implant. Blood flow in the aortic root and the washout of the sinus portion are significantly affected by aortic root morphology. CA arrives at the aortic sinus of the 2 phantoms at 0.09 s and 0.16 s after the valve opens in the symmetrical and the patient-specific phantoms, respectively. Delayed CA arrival was also observed in the patients with a transcatheter aortic valve implant. Aortic root morphology affects the blood flow in the aortic sinus and may be a factor in bioprosthetic valve thrombosis. Therefore, patient-specific aortic root morphology should be considered when selecting and positioning a prosthesis.