Numerical simulation is widely used for the assessment of aircraft aerodynamic performances and shape optimizations. Hence the objective of these simulations is often to compute aerodynamic outputs. The purpose of this thesis is to study mesh adaptation methods based on the total derivative of the outputs with respect to mesh coordinates (denoted dJ/dX). This derivative can be computed using the discrete adjoint method. The first part of this study is about the application of mesh adaptation methods applied for Eulerian flows. The mesh locations to refine are detected using a sensor based on the norm of the derivative dJ/dX. This study confirmed that this derivative is relevant in order to adapt a mesh for the computation of the output J. The second part of this work is the construction and the study of reliable criteria based on dJ/dX for both mesh adaptation and the quality assessment of a given mesh for the computation of the output J. Moreover a more efficient remeshing method based on an elliptic PDE is presented too. This new method is applied for both two-dimensional Eulerian flows and a flow described by the RANS equations. The last part of the study is devoted to the application of the proposed method to three-dimensional RANS flows on geometries of industrial interest.