The paper develops a new method of threshold setting for use in automated monitoring of a system to detect abnormal or degraded system behaviour. The method is designed for use with damage detection in time-domain methods when the model of the system is known, but it is uncertain and time-varying. The mathematical formulation of the dynamical system is based on a state-space model. Uncertainty in the system description is modelled by an unknown, norm bounded, additive perturbation of the system matrix. The method for upper bound estimates of the differences is presented. The suitability of the new method is demonstrated in damage detection example.