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A new approach of estimating the modal parameters of operating piston engines is presented. The developed approach represents a combination of concepts from currently existing analyses such as the natural excitation technique (NExT), conditioned input analysis (CIA), and conditioned source analysis (CSA), and is hence termed “conditioned NExT analysis (CNA)”. NExT analysis can be employed to estimate modal parameters of structures in their naturally excited states. However, the existence of strong combustion induced periodic forcing makes the application of NExT analysis to operating engines difficult, if not impossible. CIA and CSA, built on concepts of partial and virtual coherence respectively, can effectively condition operating engine vibration data so as to remove any periodic energy associated with the process of combustion.