An efficient method is proposed here to identify multiple damage cases in structural systems using the concepts of flexibility matrix and strain energy of a structure. The flexibility matrix of the structure is accurately estimated from the first few mode shapes and natural frequencies. Then, the change of strain energy of a structural element, due to damage, evaluated by the columnar coefficients of the flexibility matrix is used to construct a damage indicator. This new indicator is named here as flexibility strain energy based index (FSEBI). In order to assess the performance of the proposed method for structural damage detection, two benchmark structures having a number of damage scenarios are considered. Numerical results demonstrate that the method can accurately locate the structural damage induced. It is also revealed that the magnitudes of the FSEBI depend on the damage severity.