Traditional timber pagodas in Japan are believed to have high seismic performance, because there is no document of a timber pagoda, which was destroyed by earthquake. In December 2004, shaking table tests of a 1/5 scaled model of a traditional timber five storied pagoda was operated at NIED in Tsukuba. The excitations were operated 77 times on the specimen. The maximum horizontal displacement was 144.9mm (1/33rad.) measured at the top of frame, by the 1995 JMA Kobe NS input motion (maximum acceleration scaled to 2888gal). The vibration characteristics of the structure determined by shaking table tests are discussed in comparison with those by micro tremor measurements. The natural frequency of vibration in the first mode of the structure was found to be in exponential relation with the maximum horizontal displacement.