Exposure of sparsely plated endothelial cells or a wounded monolayer to shear flow induces an instantaneous inhibition of 'upstream' lamellipodial protrusion and suppresses cell migration against the flow. This phenomenon is caused by the inhibition of Rac1 activity in the upstream lamellae, as demonstrated by fluorescence resonance energy transfer experiments, and by the capacity of constitutively active Rac1 to abolish flow-induced cell polarization. The local inactivation of Rac1 coincides with rapid dephosphorylation of paxillin and the adapter protein p130CAS, which, in their phosphorylated state, participate in the activation of the Rac1 exchange factor complex DOCK180/ELMO. Indeed, overexpression of DOCK180 and ELMO rescue upstream protrusion in cells exposed to flow. Searching for the mechanosensors responsible for the polarized p130CAS dephosphorylation, we discovered that shear stress stimulates the turnover and overall growth of upstream focal adhesions, whereas downstream adhesions tend to shrink. We propose that polarized, shear stress-induced signaling from focal adhesions at the upstream lamellae, leads to the local inactivation of Rac1 by inhibiting paxillin and p130CAS phosphorylation, and consequently blocking the DOCK180/ELMO pathway.