The influence of spanwise perturbations on the transition to turbulence of a strong adverse pressure gradient (APG), laminar separated boundary layer is studied by direct numerical simulation using a high resolution numerical scheme. The perturbations are generated by positioning a discrete roughness element with a sinusoidally varying height in the spanwise direction, close to the inflow. Results indicate that the dynamics of the transition to turbulence mechanism are altered significantly due to the accelerated flow in the openings in the roughness element and the subsequent 3D instability. (C) 2015 The Authors. Published by Elsevier B.V.