Gust response analysis plays a very important role in large aircraft design. This paper presents a methodology for calculating the flight dynamic characteristics and gust response of free flexible aircraft. A multidisciplinary coupled numerical tool is developed to simulate detailed aircraft models undergoing arbitrary free flight motion in the time domain, by Computational Fluid Dynamics (CFD), Computational Structure Dynamics (CSD) and Computational Flight Mechanics (CFM) coupling. To achieve this objective, a structured, time-accurate flow-solver is coupled with a computational module solving the flight mechanics equations of motion and a structural mechanics code determining the structural deformations. A novel method to determine the trim state of flexible aircraft is also stated. First, the field velocity approach is validated, after the trim state is attained, gust responses for the one-minus-cosine gust profile are analyzed for the longitudinal motion of a slender-wing aircraft configuration with and without the consideration of structural deformation.