Most of the techniques developed to date for module performance analysis rely on steady-state measurements from a single operating point to evaluate the level of deterioration of an engine. One of the major difficulties associated with this estimation problem comes from its underdetermined nature. It results from the fact that the number of health parameters exceeds the number of available sensors. Among the panel of remedies to this issue, a few authors have investigated the potential of using data collected during a transient operation of the engine. A major outcome of these studies is an improvement in the assessed health condition. The present study proposes a framework that formalizes this observation for a given class of input signals. The analysis is performed in the frequency domain, following the lines of system identification theory. More specifically, the mean-squared estimation error is shown to drastically decrease when using transient input signals. This study is conducted with an engine model representative of a commercial turbofan.