In this paper, first we measure microtremors of wooden structures to obtain their natural frequencies. Then we construct three-dimensional structure models based on experiment data, such as beam-column connections, brace-column connections, shear walls with brace and panels, and so on. Next, we compare natural frequencies from microtremors with those acquired from eigenvalue analyses of three-dimensional structure models. We construct inverted elastic models by increasing stiffness until the natural frequency matches with the observed one. Then we examine whether the models are appropriate by comparing its nonlinear behavior with the result of a full-scale shaking table test of a wooden structure. Finally we evaluate the seismic performance of the wooden structures by using earthquake observation records and simulated strong ground motions. We confirmed that the natural periods of wooden structures obtained from microtremor linearly correlate with their wall-length ratios. We also confirmed that dynamic characteristics of structure models could be tuned up to approximate those of mirotremors. Finally we confirmed that modern wooden structures that we studies here seem to have sufficient seismic performance so that they would not be collapsed or heavily damaged for strong ground motions in the near-fault regions.