This paper examined the validity of electromagnetic radiation test to find an internal loss in columns of Japanese traditional wooden temple, Kiyomizu, in Kyoto. First, the test was performed for the specimen. The results showed that the test was able to detect 10cm over internal loss. Secondly, the test was performed for the column of Kiyomizu and some deteriorated columns were found. Finally, the earthquake response analysis was conducted for the Kiyomizu model which was assumed internal loss. In the result, the internal loss which exist column bottoms has minor influence on the seismic performance of Kiyomizu.