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A novel auto-tuning method for the Robust Inverse Dynamics Estimation (RIDE) controller algorithm is presented. The RIDE controller is applied to a high performance aircraft model. The tuner utilises a constrained genetic algorithm to automate the tuning process. The stability constraints on the algorithm ensure system stability whilst allowing for the optimum controller parameters to be selected. The results of the tuner are compared with that of another tuning method which utilises unconstrained optimisation so as to highlight the efficacy of constrained optimisation for this application. It is shown from the results that the constrained genetic algorithm optimisation scheme offers a highly effective tuning solution for the RIDE control algorithm which can be used to attain safe and high performance control.