This paper deals with the stability and transition to turbulence of wall-bounded unsteady velocity profiles with reverse flow. Such flows occur, for example, during unsteady boundary layer separation and in oscillating pipe flow. The main focus is on results from experiments in time-developing flow in a long pipe, which is decelerated rapidly. The flow is generated by the controlled motion of a piston. We obtain analytical solutions for laminar flow in the pipe and in a two-dimensional channel for arbitrary piston motions. By changing the piston speed and the length of piston travel we cover a range of values of Reynolds number and boundary layer thickness. The velocity profiles during the decay of the flow are unsteady with reverse flow near the wall, and are highly unstable due to their inflectional nature. In the pipe, we observe from flow visualization that the flow becomes unstable with the formation of what appears to be a helical vortex. The wavelength of the instability ≃3δ where δ is the average boundary layer thickness, the average being taken over the time the flow is unstable. The time of formation of the vortices scales with the average convective time scale and is ≃39/(Δū/δ), where Δu=(umax−umin) and umax, umin and δ are the maximum velocity, minimum velocity and boundary layer thickness respectively at each instant of time. The time to transition to turbulence is ≃33/(Δū/δ). Quasi-steady linear stability analysis of the velocity profiles brings out two important results. First that the stability characteristics of velocity profiles with reverse flow near the wall collapse when scaled with the above variables. Second that the wavenumber corresponding to maximum growth does not change much during the instability even though the velocity profile does change substantially. Using the results from the experiments and the stability analysis, we are able to explain many aspects of transition in oscillating pipe flow. We postulate that unsteady boundary layer separation at high Reynolds numbers is probably related to instability of the reverse flow region.