Presented is a discrete adjoint approach for computing nonlinear aeroelastic design sensitivities for transonic and viscous flows based on Reynolds Averaged Navier-Stokes computational fluid dynamic models. The method is based on a harmonic balance nonlinear frequency domain technique for modeling nonlinear aerodynamics in the frequency domain. Automatic differentiation is used to derive the computer code representing the adjoint gradient of the harmonic balance computational fluid dynamic solver. Discrete adjoint method airfoil geometric design sensitivities are demonstrated for a benchmark transonic airfoil aeroelastic configuration. Results are compared with finite-difference computations to demonstrate the accuracy of the methodology. © 2013 by Jeffrey P. Thomas, Earl H. Dowell, and Kenneth C. Hall.