The 2009 test program of E-Defense aims to investigate the new design concept compliant with high-performance expectations and long-span service life for wood structures under the act of quality assurance. This study describes the full-scale shake table test program of three-story Post and Beam (P&B) Grade-1 and Grade-2 index wood structures in the Japanese building taxonomy. Input ground motions of the test program are generated to represent a frequent, rare, and very rare level of earthquake ground motion using a random process with an envelope function. Design and analysis of test specimens were carried out following the Japanese seismic design code, where the component tests of structural elements were performed before the shake table test program. A sequence of spectrally matched artificial ground motions was used in the test program to assess the progressive collapse mechanism of both test specimens. Wall to plan ratio is a critical indicator in the structural design of wood structures to determine the minimum required amount of wall and proper plan layout on each floor. Simplified N value method and allowable stress design approach are conducted for configuring and proportioning the structural elements during the design process. Special attention is given to connection details and foundation anchorages to ensure a continuous load transfer path. The first mode-dominated response characteristics of the structure are derived from the test data. Progressive damage mechanism has yielded to cyclic strength and stiffness deterioration. The global drift angle of the test structure has exceeded the 5% drift ratio. The capability of the versatile hysteretic model for wood structures is well-justified through the comparison of the numerical model and the physical test data for collapse characterization under gradually increased earthquake demands. Accumulation of damage at the last phase of the test program is led to the loss of dynamic stability in the Grade-1 building and total collapse of Grade-2 wood-dwelling, respectively. Test results have provided valuable data to overview and improve the response characteristics of code-conforming wood structures with an extended service life towards earthquake resilience of cities.