This study utilizes a novel technique to separate and classify different ionospheric troughs from CHAMP satellite data in the winter midnight ionosphere of the southern hemisphere at high solar activity (2000–2002). The main ionospheric trough (MIT) was separated from the high latitude trough (HLT). The separation was performed through an analysis of troughs in the frame of the model of the diffuse auroral particle precipitation. Two types of HLT were distinguished. In the mid-latitude ionosphere, the MIT was separated from the ring ionospheric trough (RIT), which is formed by the decay processes of the magnetospheric ring current. The separation was performed on the basis of an analysis of the prehistory of all geomagnetic disturbances for the period under study. In addition to the RIT, an equatorward decrease in the electron density, which is superimposed on the MIT and masks it, forms quite often at American and Atlantic longitudes.