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During the 2007 Niigataken Chuetsu-oki earthquake, strong ground motion with the peak acceleration of 680cm/s/s which was larger than that of the empirical prediction was recorded at the base mat of the No.1 reactor building of Kashiwazaki-Kariwa NPS. Furthermore, in the Kashiwazaki-Kariwa NPS, over twice difference of 680 vs. 322 cm/s/s of peak acceleration between the No.1 and the No.6 reactor buildings was observed on the base mat. From the results of recent research, it is suggested that the deep sedimentary layers can be one of the important factors to elucidate these phenomena. In this study, the applicability of microtremor array measurements for estimation of deep S-wave velocity structure are discussed.