Active control of spatially evolving three-dimensional instability waves in the boundary layer of a flat plate with zero pressure gradient has been investigated both numerically and experimentally. The boundary layer was artificially excited by various computer-generated perturbations in a low-turbulence wind tunnel so as to create a three-dimensional field of instability waves. Sensors were used to detect the on-coming disturbances and appropriate control signals sent to the downstream actuators to generate counteracting disturbances. The key element of this type of active control is the determination of the transfer function of the control system connecting the sensors with the actuators. Modelling by linear theory showed that the amplitudes of the disturbances downstream were significantly suppressed when the causal transfer function was applied. To simplify the control problem different strategies using approximations to the transfer function were used. It was shown that with a very simple transfer function almost the same result could be achieved as with the full causal transfer function. The modelling was validated experimentally, first by an off-line control using different control modes, i.e. different transfer functions, and then by a real-time hardware implementation using one of the modes. Good agreement between the experimental measurements and numerical predictions indicated that a simple control strategy could be developed to inhibit the growth of the three-dimensional instability waves over extensive regions of the flow.