Planetary wave activity at quasi 16-, 10- and 5-day periods has been compared at various altitudes through the middle and upper atmosphere over Halley (76degreesS, 27degreesW), Antarctica, during the austral winters of 1997-1999. Observational data from the mesosphere, E-region ionosphere and F-region ionosphere have been combined with stratospheric data from the ECMWF assimilative operational analysis. Fourier and wavelet techniques have shown that the relationship between planetary wave activity at different altitudes is complex and during the winter eastward wind regime does not conform to a simple combination of vertical planetary wave propagation and critical filtering. Strong planetary wave activity in the stratosphere can coincide with a complete lack of wave activity at higher altitudes; conversely, there are also times when planetary wave activity in the mesosphere, E-region or F-region has no apparent link to activity in the stratosphere. The latitudinal activity pattern of stratospheric data tentatively suggests that when the stratospheric signatures are intense over a wide range of latitudes, propagation of planetary waves into the mesosphere is less likely than when the stratospheric activity is more latitudinally restricted. It is possible that, on at least one occasion, 16-day planetary wave activity in the mesosphere may have been ducted to high latitudes from the lower latitude stratosphere. The most consistent feature is that planetary wave activity in the mesosphere is almost always anti-correlated to planetary wave activity in the E-region even though the two are in close physical proximity. The oscillatory critical filtering of vertical gravity wave propagation by planetary waves and the re-generation of the planetary wave component at higher altitudes through subsequent critical filtering or breaking of the gravity waves may provide an explanation for some of these characteristics. Alternatively the nonlinear interaction between planetary waves and tides, indicated in the E-region data, may play a role.