Dynamic characteristics of structures — viz. natural frequencies, damping ratios, and mode shapes — are central to earthquake-resistant design. These values identified from field measurements are useful for model validation and health-monitoring. Most system identification methods require input excitations motions to be measured and the structural response; however, the true input motions are seldom recordable. For example, when soil–structure interaction effects are non-negligible, neither the free-field motions nor the recorded responses of the foundations may be assumed as ‘input’. Even in the absence of soil–structure interaction, in many instances, the foundation responses are not recorded (or are recorded with a low signal-to-noise ratio). Unfortunately, existing output-only methods are limited to free vibration data, or weak stationary ambient excitations. However, it is well-known that the dynamic characteristics of most civil structures are amplitude-dependent; thus, parameters identified from low-amplitude responses do not match well with those from strong excitations, which arguably are more pertinent to seismic design. In this study, we present a new identification method through which a structure's dynamic characteristics can be extracted using only seismic response (output) signals. In this method, first, the response signals’ spatial time-frequency distributions are used for blindly identifying the classical mode shapes and the modal coordinate signals. Second, cross-relations among the modal coordinates are employed to determine the system's natural frequencies and damping ratios on the premise of linear behavior for the system. We use simulated (but realistic) data to verify the method, and also apply it to a real-life data set to demonstrate its utility. Copyright © 2012 John Wiley & Sons, Ltd.