This paper presents a system identification method for multi-input, multi-output (MIMO) systems, by which a rational polynomial transfer function model is identified from experimentally determined frequency response function data. Analytically determined information is incorporated in this method to obtain a more reliable model, even in the frequency range where the excitation energy is limited. To verify the suggested method, shaking table test for an actively controlled two-story, bench-scale building employing an active mass damper is conducted. The results show that the proposed method is quite effective and robust for system identification of MIMO systems.