In recent years it has become clear that cell signalling pathways are not simple linear chains of events as was once thought but frequently diverge, converge and employ positive and negative feedback. As a result signals show a complex pattern of spatial and temporal activity that is difficult to explain despite a wealth of experimental data. Systems Biology attempts to predict and understand the behaviour of complex systems by integrating information from diverse sources and principles drawn from a large number of different scientific disciplines. The signalling pathways regulating endothelial responses to shear stress have been extensively studied, since perturbed fluid flow contributes significantly to the development of heart disease. Shear stress activates many signals in endothelial cells, from ion influxes to protein phosphorylation and gene expression, and induces changes in endothelial morphology. Here a modelling and Systems Biology approach was taken to investigate and understand better the endothelial signal transduction networks that convert fluid flow stimulation into biochemical signals. A static signal transduction network was built from integrin cell surface receptors to activation of the tyrosine kinases focal adhesion kinase (FAK) and Src. Parameters for each reaction in this network were collected from the literature or, when necessary, estimated. To model how fluid flow initiates signalling in this network, the shear stress-induced calcium influx and the viscoelastic response of transmembrane receptors such as integrins to mechanical force were examined by means of mathematical modelling, using ordinary differential equations. These effects were used as primary activators of the shear stress response in endothelial cells, allowing quantitative analysis of the intracellular signal transduction flow which propagates from integrin to paxillin, FAK and Src activation. The magnitude and dependencies of each influence were examined individually and in conjunction with each other. The model was used to investigate the role and dynamic regulation of previously unstudied molecules in the network and the simulated results were compared against experimental data in order to validate hypotheses and increase our understanding of the molecular processes underlying the shear stress response.