This paper describes the design, test and validation processes of a dynamic identification algorithm aimed at the time-dependent assessment of modern structures and heritage buildings for civil and seismic engineering purposes. Full validation of the algorithm is performed through analysis of numerically simulated data from an idealized masonry tower. Making use of output-only vibration measurements, the non-parametric algorithm can generate dynamic features results as time-dependent functions for the complete observation period. The algorithm can work in the presence of different dynamic loads and non-linear structural behaviours, close spectral frequency components and noisecontaminated data. Time-dependent structural dynamic parameters that can be computed are modal frequencies, modal displacements, modal curvatures, and higher derivatives of mode shapes. The proposed algorithm aims to be used as the core estimator of timedependent identification methods devoted to the health monitoring of structures and infrastructures, being suitable for a multitude of tasks ranging from the simple operational modal analysis (in pre and post-event condition) to the complex online assessment of the structural response during seismic events for rapid damage identification.[1,2,3]. Traditional dynamic identification methods used in Operational Modal Analysis (OMA) can accurately estimate parameters like modal frequencies, damping ratios and mode shapes [4,5,6], but some methods present problems related to the difficulties in identifying close-spaced modes or uncertainties when working with noise-contaminated measurements [7,8,9]. On the other hand, most methods based on output-only data work with parametric eigenvalue decompositions of a weighted data matrix, like the Singular Value Decomposition (SVD) of the Power Spectral Density matrix (PSD) -as far as the Frequency Domain Decomposition (FDD) methods are concerned [10,11,12] -or the SVD of Hankel matrixes in case of Stochastic System Identification methods (SSI) [13,14,15]. Thus, they are restricted to the linear-elastic range (no-damage, no-yielding) and are not suitable to identify dynamic features in the presence of nonlinearities. Moreover, these methods cannot generate results as time-dependent functions since they are limited to the comparative assessment between different structural conditions (usually before and after a particular event), thereby being unable to provide any information about the actual temporal evolution of dynamic parameters like natural frequencies and mode shapes during the damage progress. To effectively upgrade stateof-the-art dynamic identification techniques for SHM intents, performing dynamic identification in the presence of nonlinearities and tracking relevant time-dependent modal parameters are essential tasks to accomplish [16,17,18,19]. The development, testing and preliminary validation of a non-parametric algorithm suitable for this purpose are hereby presented. The proposed algorithm is capable of processing linear (no damage) and non...