In this study, vibration responses of harbor caisson structures with various boundary conditions are experimentally examined as a fundamental study to develop a health assessment technique for harbor structures. To achieve the objective, four-step approach is implemented. Firstly, a target caisson structure is selected and a small-scale model of the caisson model is constructed in the laboratory. Secondly, a finite element model of the caisson model is generated to analyze dynamic responses of the structure. Thirdly, experimental tests are performed on the caisson model to obtain dynamic responses under various boundary conditions and impact locations. Four different boundary conditions, 1) ‘hanging by crane’, 2) ‘standing on styrofoam block’, 3) ‘standing on sand mat’, and 4) ‘standing on concrete floor’ are considered. Finally, variation of frequency response ratio assurance criterion and correlation coefficients of frequency response functions are analyzed.