A frequency-domain method for estimating the mass, stiffness and damping matrices of the model of a structure is presented. The developed method is based on our previous work on the extraction of normal modes from the complex modes of a structure. A transformation matrix is obtained from the relationship between the complex and the normal frequency response functions of a structure. The transformation matrix is employed to calculate the damping matrix of the system. The mass and the stiffness matrices are identified from the normal frequency response functions by using the least squares method. Two simulated systems are employed to illustrate the applicability of the proposed method. The results indicate that the damping matrix can be identified accurately by the proposed method. The reason for the good results is that the damping matrix is identified independently from the mass and the stiffness matrices. In addition, the robustness of the new approach to uniformly distributed measurement noise is also addressed.