Scintillation observations at VHF and UHF frequencies at auroral and subauroral stations, together with in situ measurements by ISIS 2 in 1971--1972 and S3-2 in 1975--1976, show two aread of irregularities during magnetic storms. The two regions are related to the plasmapause and to the auroral oval and straddle the minimum electron density region of the trough. The plasmapause irregularities are located on the equatorward edge of the trough and may extend several degrees in latitude. The electron density trough itself shows very low activity of irregularities, while the poleward wall of the trough is the beginning of the region where auroral oval F layer irregularities are present. By use of S3-2 observations of electron and ion density, electron temperature, magnetic fields, and precipitating particles, it is suggested that the production mechanism of the plasmapause irregularities is the temperature gradient drift instability. It is also shown that auroral irregularities are closely related to field-aligned currents.