This paper describes the implementation of system identification and controller design techniques using model predictive control (MPC) for wind turbines with distributed active flaps for load control. An aeroservoelastic model of the 5 MW NREL/Upwind reference wind turbine, implemented in the code DU_SWAMP, is used in an industry‐based MPC controller design cycle, involving the use of dedicated system identification techniques. The novel multiple‐input multiple‐output MPC controllers, which incorporate flap actuator constraints and the use of local inflow measurement signals, are designed and implemented for various operating points. The controllers are evaluated in standard power production load cases and fatigue load reductions up to 27.3% are achieved. The distributed flaps controller scheme is also compared with simpler single‐flap single‐input single‐output and individual pitch controller schemes. Copyright © 2011 John Wiley & Sons, Ltd.