The feasibility of a vibration-based damage identification approach for impact damage in two advanced composite skin-stiffener structures is investigated in this paper. Mode shape curvatures combined with the modal strain energy damage index (MSE-DI) algorithm are utilized to identify the damage. Special attention is paid to the effective application of this vibration-based methodology by investigating the relation between the damage location, the structural design, and the dynamic behavior. The performance of a 1D and 2D formulation of the MSE-DI algorithm is compared for several damage scenarios. Experiments demonstrated the capabilities of the MSE-DI algorithm to detect, localize, and roughly quantify the size of barely visible impact damage in advanced composite structures. It is concluded that the method is particularly effective for health monitoring of skin-stiffener connections. The most effective results were obtained by considering the 1D formulation in the direction of the stiffeners for the stiffener mid-section and perpendicular to the stiffeners for the stiffener run-out. The method remained inconclusive in the case of pure skin-related damage. The results obtained in this study contribute to the development of guidelines for vibration-based structural health monitoring of advanced composite skin-stiffener structures.