Abstract. This article presents an identification algorithm dedicated to the modal analysis of aircraft structures during flighttests. More specifically, this algorithm was designed to process short duration tests carried out with multi-input excitations. The identification problem is solved in the frequency domain and the limit effects are considered so as to avoid transient effects with short data sequences. To minimise the effects of the noise, a non-linear gradient-based optimisation method is used. Its performance is improved by the use of an appropriate over-parametrised matrix fraction descriptions. Because the cost function to be minimised is non-convex, this method is however sensitive to the initialisation. For this reason, an iterative instrumental variable method is used to find an initial estimate. This one gives a value of the cost-function sufficiently close to its global minimum so as to ensure a fast convergence of the optimisation. Thus, the algorithm presented in this article is a combination of two iterative methods that gives accurate mode estimations even with high level of noise, as shown on an illustrative example.