The aeroelastic and aerothermoelastic behavior of three-dimensional configurations in hypersonic flow regime are studied. The aeroelastic behavior of a low aspect ratio wing, representative of a fin or control surface on a generic hypersonic vehicle, is examined using third order piston theory, Euler and Navier-Stokes aerodynamics. The sensitivity of the aeroelastic behavior generated using Euler and Navier-Stokes aerodynamics to parameters governing temporal accuracy is also examined. Also, a refined aerothermoelastic model, which incorporates the heat transfer between the fluid and structure using CFD generated aerodynamic heating, is used to examine the aerothermoelastic behavior of the low aspect ratio wing in the hypersonic regime. Finally, the hypersonic aeroelastic behavior of a generic hypersonic vehicle with a lifting-body type fuselage and canted fins is studied using piston theory and Euler aerodynamics for the range of 2.5 ≤ M ≤ 28, at altitudes ranging from 10,000 feet to 80,000 feet. This analysis includes a study on optimal mesh selection for use with Euler aerodynamics. In addition to the aeroelastic and aerothermoelastic results presented, three time domain flutter identification techniques are compared, namely the moving block approach, the least squares curve fitting method, and a system identification technique using an Auto-Regressive model of the aeroelastic system. In general, the three methods agree well. The system identification technique, however, provided quick damping and frequency estimations with minimal response record length, and therefore offers significant reductions in computational cost. In the present case, the computational cost was reduced by 75%. The aeroelastic and aerothermoelastic results presented illustrate the applicability of the CFL3D code for the hypersonic flight regime.