Abstract A new general formulation that is applicable to the damaged, linear elastic structures ‘unified framework’ is used to obtain analytical expressions for natural frequencies and mode shapes. The term mode shapes is used to mean the displacement modes, the section rotation modes, the sectional bending strain modes and sectional shear strain modes. The formulation is applicable to damaged elastic self-adjoint systems. The formulation has two unique aspects: First, the theory is mathematically rigorous since no assumptions are made regarding the physical behavior at a damage location, therefore there is no need to substitute the damage with a hypothetical elastic element such as a spring. Since the beam is not divided at the damage location, rather than an 8 by 8, only a 4 by 4 matrix is solved to obtain the natural frequencies and mode shapes. Second, the inertia effects due to damage which have till now been neglected by researchers are accounted for. The formulation uses a geometric damage model, perturbation of mode shapes and natural frequencies, and a modal superposition technique to obtain and solve the governing differential equation. Timoshenko beam theory is then taken as an example, and its results are compared with results using Euler–Bernoulli beam theory and finite element models. The range of applicability of the two theories is ascertained for damage characteristics such as depth and extent of damage and beam characteristics such as slenderness ratio and Poisson׳s ratio. The paper considers rectangular notch like non-propagating damage as an example of the damage.