Patient-specific computational fluid dynamics (CFD) is a powerful tool for researching the role of blood flow in disease processes. Modern clinical imaging technology such as MRI and CT can provide high resolution information about vessel geometry, but in many situations, patient-specific inlet velocity information is not available. In these situations, a simplified velocity profile must be selected. We studied how idealized inlet velocity profiles (blunt, parabolic, and Womersley flow) affect patient-specific CFD results when compared to simulations employing a “reference standard” of the patient’s own measured velocity profile in the carotid bifurcation. To place the magnitude of these effects in context, we also investigated the effect of geometry and the use of subject-specific flow waveform on the CFD results. We quantified these differences by examining the pointwise percent error of the mean wall shear stress (WSS) and the oscillatory shear index (OSI) and by computing the intra-class correlation coefficient (ICC) between axial profiles of the mean WSS and OSI in the internal carotid artery bulb. The parabolic inlet velocity profile produced the most similar mean WSS and OSI to simulations employing the real patient-specific inlet velocity profile. However, anatomic variation in vessel geometry and the use of a nonpatient-specific flow waveform both affected the WSS and OSI results more than did the choice of inlet velocity profile. Although careful selection of boundary conditions is essential for all CFD analysis, accurate patient-specific geometry reconstruction and measurement of vessel flow rate waveform are more important than the choice of velocity profile. A parabolic velocity profile provided results most similar to the patient-specific velocity profile.