This article presents identification algorithms dedicated to the modal analysis of civil aircraft structures during in-flight flutter tests. This particular operational framework implies several specifications for the identification procedure. To comply with these requirements, the identification problem is formulated in the frequency domain as an output-error problem. Iterative identification methods based on structured matrix fraction descriptions are used to solve this problem and to identify a continuous-time model. These iterative methods are specifically designed to deal with experiments where short-duration tests with multiple-input excitations are used. These algorithms are first discussed and then evaluated through a simulation example illustrative of the in-flight modal analysis of a civil aircraft. Based on these evaluation results, an efficient iterative algorithm is suggested and applied to real flight-test data measured on board a military aircraft.