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This paper presents a real time state estimation algorithm for control and security maintenance of multi-converter MES power electronic systems. Estimation of the state variables of the system includes the effects of ripples and converter switching actions. The proposed state estimator is based on the weighted least squares (WLS) approach. Generalized state space averaging technique in which we consider the DC value of the state variables and their harmonics is used to model DC/DC converters for the state estimator. In this paper, after introducing the proposed approach and the concept of security and control assessments, results of applying the proposed method to a representative system are presented.