Clinical research has historically focused on the two main strategies of in vivo and in vitro experimentation. The concept of applying scientific theory to direct clinical applications is relatively recent. In this paper we focus on the interaction of wall shear stress with the endothelium and discuss how ‘state of the art’ computer modelling techniques can provide valuable data to aid understanding. Such data may be used to inform experiment and further, may help identify the key features of this complex system. Current emphasis is on coupling haemodynamics with models of biological phenomena to test hypotheses or predict the likely outcome of a disease or an intervention. New technologies to enable the integration of models of different types, levels of complexity and scales, are being developed. As will be discussed, the ultimate goal is the translation of this technology to the clinical arena.