Identification of nonlinear processes in the presence of noise corrupted and correlated multiple scheduling variables with missing data is concerned. The dynamics of the hidden scheduling variables are represented by a state-space model with unknown parameters. To assure generality, it is assumed that the multiple correlated scheduling variables are corrupted with unknown disturbances and the identification dataset is incomplete with missing data. A multiple model approach is proposed to formulate the identification problem of nonlinear systems under the framework of the expectation-maximization algorithm. The parameters of the local process models and scheduling variable models as well as the hyperparameters of the weighting function are simultaneously estimated. The particle smoothing technique is adopted to handle the computation of expectation functions. The efficiency of the proposed method is demonstrated through several simulated examples. Through an experimental study on a pilot-scale multitank system, the practical advantages are further illustrated. (c) 2015 American Institute of Chemical Engineers AIChE J, 61: 3270-3287, 2015