Laminar-to-turbulent transition in pulsatile flow through a stenosis is studied by means of three-dimensional numerical simulations. The flow transition is associated with the occurrence of a flow instability initiating in the stenosis region. The instability is manifested by a three-dimensional symmetry-breaking and leads to asymmetric separation and intense swirling motion downstream of the stenosis. The above have profound effects on the wall shear stress (WSS). The simulations reveal that the asymmetric separation is extended several radii downstream of the stenosis with substantial WSS fluctuations, in both space and time, occurring in the poststenotic region.