In this paper, performance of aortic heart valve prosthesis in different geometries of the aortic root is investigated experimentally. The objective of this investigation is to establish a set of parameters, which are associated with abnormal flow patterns due to the flow through a prosthetic heart valve implanted in the patients that had certain types of valve diseases prior to the valve replacement. Specific valve diseases were classified into two clinical categories and were correlated with the corresponding changes in aortic root geometry while keeping the aortic base diameter fixed. These categories correspond to aortic valve stenosis and aortic valve insufficiency. The control case that corresponds to the aortic root of a patient without valve disease was used as a reference. Experiments were performed at test conditions corresponding to 70 beats/min, 5.5 L/min target cardiac output, and a mean aortic pressure of 100 mmHg. By varying the aortic root geometry, while keeping the diameter of the orifice constant, it was possible to investigate corresponding changes in the levels of Reynolds shear stress and establish the possibility of platelet activation and, as a result of that, the formation of blood clots.