In this article a Model Predictive Control (MPC) strategy for the trajectory tracking of an unmanned quadrotor helicopter is presented. The quadrotor’s dynamics are modeled by a set of Piecewise Affine (PWA) systems around different operating points of the translational and rotational motions. The proposed control scheme is dual and is consisted by an integral MPC for the translational motions, followed by a MPC–scheme for the quadrotor’sattitude motions’ tracking. By the utilization of PWA representations, the controller is computed for a larger part of the quadrotor’s flight envelope. Theproposed dual control scheme is able to calculate optimal control actions with robustness against atmospheric disturbances (e.g. wind gusts) and physical constraints of the quadrotor (e.g. maximum lifting forces or fixed thrust limitations in order to extend flight endurance). Extended simulation studies prove the efficiency of the MPC–scheme, both in trajectory tracking and aerodynamic disturbances attenuation.