The most widely known form of multifunctional aircraft structure is smart structures for structural health monitoring (SHM). The aim is to provide automated systems whose purposes are to identify and to characterize possible damage within structures by using a network of actuators and sensors. Unfortunately, environmental and operational variability render many of the proposed damage detection methods difficult to successfully be applied. In this paper, an original robust damage detection approach using output-only vibration data is proposed. It is based on independent component analysis and matrix perturbation analysis, where an analytical threshold is proposed to get rid of statistical assumptions usually performed in damage detection approach. The effectiveness of the proposed SHM method is demonstrated numerically using finite element simulations and experimentally through a conformal load-bearing antenna structure and composite plates instrumented with piezoelectric ceramic materials.