The structural responses and vibration properties such as frequencies and mode shapes are directly related to the structural mass and stiffness. Changing structural conditions will affect the structural responses and vibration properties. Structural conditions can thus be identified through measurements of structural vibration. However, certain uncertainties associated with structure models, changing ambient environmental conditions, changing loading conditions, equipment noises and various signal processing techniques used in extracting structural vibration properties, etc. is inevitable. The influences of these uncertainties on structural vibration properties might be more significant than that of the structural damage, therefore, cause false identification or result in the true structural damage not identifiable. This paper studies the applicability and reliability of a few popularly used modal identification methods including time-domain, frequency-domain and time-frequency domain methods for civil structural system identification. The results indicate that on average a 2% to 3% error tends to be yielded by using different signal processing techniques for vibration frequencies identification when the signal is not heavily noise contaminated, which should be taken into account when estimating the damage detection results. The applicability of the time-frequency domain methods to the identification of time-varying system either with sudden change or continuous variance is also discussed. © Institution of Engineers Australia, 2013.