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 identifi ed 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 infl uences of these uncertainties on structural vibration properties might be more signifi cant than that of the structural damage, therefore, cause false identifi cation or result in the true structural damage not identifi able. This paper studies the applicability and reliability of a few popularly used modal identifi cation methods including time-domain, frequencydomain and time-frequency domain methods for civil structural system identifi cation. The results indicate that on average a 2% to 3% error tends to be yielded by using different signal processing techniques for vibration frequencies identifi cation 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 identifi cation of time-varying system either with sudden change or continuous variance is also discussed.