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In ship structures, many parts are in contact with inner or outer fluid as stern, ballast and oil tanks. Fatigue damages can be sometimes observed in these tanks which seem to be caused by resonance. Tank structures in ships are in contact with water and the vibration characteristics are strongly affected by the added mass of containing water. Therefore it is important to predict vibration characteristics of tank structures. In order to estimate the vibration characteristics, the fluid-structure interaction problem has to be solved precisely. In the present paper, we have developed a numerical tool of vibration analysis of 3-dimensional tank structures using finite elements for plates and boundary elements for water region. To verify the present analysis, we have made an experiment for vibration characteristics of a tank with elastic opposite panels. And the added mass effect of containing water and the effect of structural constraint between panels are investigated numerically and discussed.