Intense atmospheric vortices of all types are not homogenous along their vertical axis, but rather have considerable variation of their wind and density fields with height. Furthermore, their interaction with the surface leads to the development of a swirling boundary layer which gives rise, especially in the cases of tornadoes and hurricanes, to a substantial secondary circulation which plays a crucial role in the formation and maintenance of the inner core structure of the vortex. With these facts in mind, we have developed a methodology that allows for the linearized stability analysis of truly three dimensional (but axisymmetric) intense atmospheric vortices with realistic wind and density profiles. The methodology also allows for the inclusion of the secondary circulation. We will present the results of stability analyses of idealized hurricanes, hurricane wind fields generated from mesoscale models, and tornado-like wind fields generated from simple numerical models.