Dynamic properties of a structure tested using a shake table could be estimated correctly, if one uses an appropriate transfer function between the structural motion and table motion measured. A unique method to construct the transfer function including the effect of rocking motion of the three-dimensional (3D) shake table is proposed. By using an analytical model of five-story building, the method is shown to be much more accurate than the conventional method that considers table motions of only the horizontal direction. The method is also applied to estimate equivalent linear modal properties of a full-scale five-story building tested by using the E-Defense, the world's largest 3D shake table. Different cases of the building having linear dampers, nonlinear dampers, or no dampers, with elastic or slightly yielding frame are considered, and applicability of the method discussed.