This paper presents a comparison of linear and non-linear methods for the analysis of aeroelastic behaviour and flutter boundary prediction. The methods in question include NASTRAN and ZAERO, based on linear aerodynamics, and the non-linear coupled CFD-CSD methods RANSMB and PMB, developed at the Universities of Bristol and Glasgow respectively. The test cases used for this comparison are the MDO and AGARD 445.6 weakened wing. In general, it was found that the non-linear methods demonstrate excellent agreement with respect to pressure distributions, deflections, dynamic behaviour, and flutter boundary locations for both cases. This is in contrast to previous studies involving similar methods, where notable differences across the MDO span were found, and is taken to imply good performance of the CFD-CSD interpolation schemes employed here. While the linear methods produce similar flutter boundaries to the coupled codes for the aerodynamically simple AGARD 445.6 wing, results for the transonic ‘rooftop’ MDO wing design did not agree as well.