This paper deals with constant disturbances rejection in limit cycle tracking for an under-actuated mechanical system. The feedback controler presented in [1] is enhanced to handle constant disturbances by using online iterative estimation of an equivalent disturbance which is easily compensated by adding the estimated value to the output of the system. The effectiveness of the proposed method is demonstrated through real-time experiments on an inertia wheel inverted pendulum. Constant disturbances are introduced either as a weight asymmetrically fixed to the pendulum body, or by the use of a bad calibrated sensor.