Knowledge of the upper atmosphere state, and in particular of the ionosphere, is essential in several applications such as systems used in radio frequency communications, satellite positioning and navigation. In general, these systems depend on the ionosphere, involving it as part of the system or as an interference source. In all the cases an essential task is determining the path and modifications of ray propagation through the ionospheric plasma. The ionospheric refractive index and the maximum usable frequency MUF that can be received over a given distance, are key parameters which in general are simplified neglecting the Earth’s magnetic field effect. The value of M(3000)F2, related to the MUF that can be received over 3000 km is routinely scaled from ionograms using a technique which also neglects the geomagnetic field effect assuming a standard simplified propagation model. M(3000)F2 should be affected then by a systematic trend linked to the Earth’s magnetic field secular variation. On the other hand, among the upper atmosphere effects expected from increasing greenhouse gases concentration is the lowering of the F2-layer peak density height, hmF2. This ionospheric parameter is usually estimated using the M(3000)F2 factor, so it would also carry this “systematic trend”. The magnitude of the geomagnetic field effect on MUF estimations is assessed as well as the consequences of this effect on hmF2 long-term trend estimations, which, at some locations, can be significant in comparison to the few kilometers decrease expected from greenhouse gases effect.