The Church of Gesù and the tower of the Cathedral were stricken and damaged by Emilia-Romagna earthquake sequence of May 2012. This paper presents the procedure for the structural identification of the most widespread types of religious monuments. The dynamic behavior was analyzed using the ambient vibrations test to measure the dynamical properties (mode of vibration, frequencies, displacements and damping ratios) of the constructions using a modal identification of output-only systems. The operational modal analysis OMA has been carried out to identify the modal characteristics through poly-reference Least Square Complex Frequency-domain (pLSFC) estimator. The global structural health monitoring was carried out to define the real dynamic behavior of the damaged constructions that are subjected to different mechanism. These researches are useful for the structural rehabilitation and to define the possible changes in the structural behavior.