The paper presents the dynamic structural health monitoring activities on Saint Torcato church, in Guimarães, Portugal, which has significant structural problems due to soil settlements. Cracks can be observed on the main and the lateral façades, the bell-towers are leaning, and the arches in the nave exhibit a failure mechanism with cracks and vertical deformations. These phenomena are progressing and a structural intervention is planned. A monitoring system has been installed to control the current condition and to assess the success of the future intervention. The paper shows the monitoring results with an emphasis in the dynamic analysis carried out before the structural strengthening, namely with respect to: experimental tests with output-only techniques for frequencies, damping and mode shapes estimation, FE model updating analysis and dynamic monitoring. The automatic system identification process uses ambient vibration signatures in combination with cluster analysis and rule-based approach for the interpretation of the results of the Stochastic Subspace Identification method. © 2012 Elsevier Ltd. All rights reserved.