The paper explores the potential of a low-cost advanced video-based technique for the assessment of structural damage induced to buildings by seismic loading. A low-cost high-speed video camera was utilized for motion magnification (MM) processing of footages of a two-story reinforced concrete frame building subjected to shaking table tests. The damage after seismic loading was estimated by analyzing the dynamic behavior (i.e. in terms of modal parameters) and the structural deformations of the building in the MM videos. The results by MM were compared for method validation to damage assessment obtained by the analyses of conventional accelerometers and high-precision optical markers tracked by a passive 3D motion capture system. Also, 3D laser scanning to obtain an accurate survey of the building geometry before and after the seismic tests was carried out. In particular, accelerometers were also processed and analyzed by using several stationary and non-stationary techniques with the aim to analyze the linear behavior of the undamaged structure and the nonlinear structural behavior during damaging shaking table tests. The proposed MM-based procedure provided accurate estimate of the main modal frequency and the damage location through the analysis of modal shapes, which were confirmed by advanced analyses of accelerometric data.