Recently, the Hilbert-Huang transform (HHT) has gained considerable attention as a novel technique of signal processing, which shows promise for the system identification and damage detection of structures. This study investigates the effectiveness and accuracy of the HHT method for the system identification and damage detection of structures through a series of experiments. A multi-degree-of-freedom (MDOF) structural model has been constructed with modular members, and the columns of the model can be replaced or removed to simulate damages at different locations with different severities. The measured response data of the structure due to an impulse loading is first decomposed into modal responses using the empirical mode decomposition (EMD) approach with a band-pass filter technique. Then, the Hilbert transform is subsequently applied to each modal response to obtain the instantaneous amplitude and phase angle time histories. A linear least-square fit procedure is used to identify the natural frequencies and damping ratios from the instantaneous amplitude and phase angle for each modal response. When the responses at all degrees of freedom are measured, the mode shape and the physical mass, damping and stiffness matrices of the structure can be determined. Based on a comparison of the stiffness of each story unit prior to and after the damage, the damage locations and severities can be identified. Experimental results demonstrate that the HHT method yields quite accurate results for engineering applications, providing a promising tool for structural health monitoring.