A class of modified state space self-tuning controllers of the minimum state error variance type was considered. A suitable chosen structure of the proposed controller allows the tracking of a time-varying reference input and makes it possible to apply this solution to nonlinear and non-stationary plants. The advantage in using the proposed algorithm for nonlinear system control is demonstrated through its application to aircraft control around a prespecified reference trajectory in the presence of characteristic disturbances. The results show that the proposed controller has good tracking performance and possesses rather good immunity towards disturbances.