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Parameters of background variations of FoF2 critical frequency in the 1−4mHz frequency range are studied. For that, a technique of automatic detection of critical frequency fromthe ionograms is developed. The background variations of FoF2 frequency was compared with the Pc5/Pi3 geomagnetic pulsations in on the ground and the magnetosphere. It was found, that Pc5/Pi3 fluctuations of F0f2 are predominantly registered in the afternoon MLT sector under weak and moderate magnetic disturbances. Background variations of FoF2 are in the majority of cases decoupled from the Pc5/Pi3 on the ground. The fraction of coherent geomagnetic and F0f2 pulsations is higher for the geomagnetic pulsations registered in the magnetosphere, than on the ground. Case studies showed coherent pulsations simultaneously registered in the magnetic field and particle flux at THEMIS satellite located in the night magnetosphere and FoF2 in Sodankyla. Meanwhile, we have found no correspondence in geomagnetic pulsations at Sodankula. This effect is probably related to screening of small-scale MHD waves by the ionosphere.