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The main goal of the paper is to test the Embedded Model Control (EMC) design and implementation on a typical underactuated apparatus, like the Furuta pendulum, by comparing experimental results with a Linear Quadratic Regulator (LQR). EMC can be considered as a disturbance rejection control strategy, since the state predictor is extended to explicitly include disturbance dynamics, in charge of predicting the uncertainty to be rejected by control law. Essential in EMC design is the separation between controllable and not controllable dynamics, a task which allows us to find the controllable channel of underactuated systems from the low-dimensional command to the whole system degrees of freedom (DF). Pursuing this objective, a rather generic method is shown, which is applicable to other underactuated systems. The result is a very simple controllable dynamics from the single pendulum command to pendulum DF arranged in a single series of controllable integrators. The neglected feedback channels, including the unstable gravity feedback, are treated as unknown thus posing a challenge to disturbance prediction and closed loop stability. Typical in EMC, closed loop eigenvalues are chosen to guarantee stability, a pre-requisite to performance. Experimental results point out effectiveness and advantage, with respect to LQR, of design and implementation under adverse conditions, due to a disturbance pulse, in which command saturates. • Model-based framework Embedded Model Control is developed for underactuated systems. • Controllable system is transformed into a series of integrators from command-output. • Two decoupled dynamic feedback low order noise/disturbance observers are designed. • Stability is analysed by measurement law and the control law, designed separately. • Experimental tests are done on the Furuta Pendulum showing requirements are achieved. [ABSTRACT FROM AUTHOR]