Direct numerical simulation of the incompressible Navier-Stokes equations is used to study flows where laminar boundary-layer separation is followed by turbulent reattachment forming a closed region known as a laminar separation bubble. In the simulations a laminar boundary layer is forced to separate by the action of a suction profile applied as the upper boundary condition. The separated shear layer undergoes transition via oblique modes and Λ-vortex-induced breakdown and reattaches as turbulent flow, slowly recovering to an equilibrium turbulent boundary layer. Compared with classical experiments the computed bubbles may be classified as ‘short’, as the external potential flow is only affected in the immediate vicinity of the bubble. Near reattachment budgets of turbulence kinetic energy are dominated by turbulence events away from the wall. Characteristics of near-wall turbulence only develop several bubble lengths downstream of reattachment. Comparisons are made with two-dimensional simulations which fail to capture many of the detailed features of the full three-dimensional simulations. Stability characteristics of mean flow profiles are computed in the separated flow region for a family of velocity profiles generated using simulation data. Absolute instability is shown to require reverse flows of the order of 15–20%. The three-dimensional bubbles with turbulent reattachment have maximum reverse flows of less than 8% and it is concluded that for these bubbles the basic instability is convective in nature.