The aim of structural health monitoring for civil structures is not only detection of sudden or progressive damages but also monitoring their performance under operational conditions or under some particular environmental issues such as earthquakes. Seismic protection of buildings at risk can be reached increasing the knowledge of the structural behavior of existing constructions. This circumstance points out the opportunity of monitoring the performance of civil structures over their operational lives. The present paper deals with automated Structural Health Monitoring (SHM) technologies adopted for the School of Engineering Main Building at the University of Naples “Federico II”. In particular, the attention is focused on the development of an automated procedure based on the Operational Modal Analysis (OMA) that must ensure the continuous monitoring and extraction of the modal parameters of the building. Some numerical examples are then discussed in order to point out effectiveness of the algorithm and relevant issues that need to be improved.