Direct numerical simulations were employed to investigate the effects of free-stream turbulence on the control of laminar boundary-layer separation using pulsed vortex generator jets. Earlier research has shown that laminar separation can efficiently and effectively be controlled when an inviscid shear-layer instability is exploited. This paper addresses the question if such a control remains effective under free-flight conditions, which are characterized by free-stream turbulence. In the direct numerical simulations isotropic free-stream turbulence was introduced at the inflow boundary. For low free-stream turbulence levels and a blowing ratio of 0.6 the pulsed jets showed the same effectiveness as observed in earlier research with zero free-stream turbulence. When the free-stream turbulence intensity was increased to 3% the effectiveness of the pulsed jets slowly diminished. A proper orthogonal decomposition of the time-dependent data revealed that the dominant flow structures are two-dimensional for low to moderate free-stream turbulence levels. For 3% turbulence intensity the dominant structures were streamwise- "streaky" structures. Additional simulations with higher blowing ratios were carried out for 3% free-stream turbulence. When the blowing ratio was increased to 1.5 the separation length was reduced. For larger blowing ratios the separation length remained constant. For a blowing ratio of 2.5 the most energetic flow structures were predominantly two-dimensional.