The article presents issues related to the application of a moving horizon estimator for state variables reconstruction in an advanced control structure of a drive system with an elastic joint. Firstly, a short review of the commonly used methods for state estimation in presented. Then, a description of a state controller structure follows. The design methodology based on the poles-placement method is briefly described. Next, the mathematical algorithm of MHE is presented and some crucial features of MHE are analysed. Then, selected simulation and experimental results are shown and described. The investigation shows, among others, the influence of window length on the quality of state variables estimation.