Starting from results obtained in the topology optimization of two Airbus pylons, this paper proposes an innovative bi-level optimization scheme used to solve multidisciplinary optimization problems including aerodynamics (drag) and structure (mass, stiffness) requirements. The drag related to the pylon fairing depends on some global geometric design variables. For a given geometry, the minimal mass is obtained by solving a topology optimization problem with stiffness (displacement) restrictions. Mass and drag feed a cost function which is minimized with a surrogate-based optimization approach. The developed methodology is demonstrated for the multidisciplinary optimization of the Airbus pylon.