Modem aircraft are under a severe operating environment, in which uncertainties in mass, stiffuess, and aerodynamic characteristics could play an important role in determining the safety ofan airplane. Recently, several analysis methodologies have been proposed to find a new critical flight condition in the presence of the system uncertainties. In the present paper, a variation is assumed to exist in the aerodynamic characteristics. A robust aeroelastic analysis is established which accounts for aerodynamic variation due to a different level of compressibility and atmospheric density. Mathematically, the variations in Mach number and atmospheric density are treated as aerodynamic uncertainties. A robust flutter stability boundary is obtained by using the mu method. It is found that the worst case flutter speed, dynamic pressure, and atmospheric density results are all more conservative than the nominal flutter results.