This paper presents an experimental modal analysis of a caisson-type breakwater to produce basic information for the structural health assessment of a caisson structure. To achieve the objective, the following approaches are implemented. First, modal analysis methods are selected to examine the modal characteristics of a caisson structure. Second, experimental modal analyses are performed using finite element analyses and lab-scale model tests. Third, damage scenarios that include several damage levels in a foundation-structure interface are designed. Finally, the effects of damage on the modal characteristics are analyzed for the purpose of utilizing them for damage identification.