An examination of the dynamics of the middle atmosphere as reconstructed in the NASA Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2) reveals the formation of large scale three dimensional vortices in the tropical stratosphere following both the vernal and autumnal equinoxes at times where the jet associated with the westerly phase of the semi-annual oscillation (SAO) is maximal and extratropical influences from planetary waves are weakest. An empirical orthogonal function (EOF) analysis of the second matrix invariant of the velocity gradient tensor applied to the shear zones about the SAO reveals statistically stationary wave-5 vortex structures that span more than 3200km in length and up to 40km in the vertical. Eliassen-Palm fluxes suggests the vortices are maintained by a combination of local (shear zones) and remote (vertically propagating tropical) sources of momentum. These large scale coherent features appear to be unique to the stratopause.