[1] A systematic analysis of the thermospheric density response to changes in the interplanetary magnetic field (IMF) sector polarity is carried out. For this purpose we use a high-latitude southern thermospheric total mass density near 400 km altitude, derived from the high-accuracy accelerometer on board the Challenging Minisatellite Payload (CHAMP) spacecraft in 2003, a period of a well-defined IMF sector polarity change. The IMF sector polarity changes appear to strongly influence the high-latitude thermospheric density variations, especially in equinox seasons. After normalization to a constant solar flux level, densities in the Southern Hemisphere near the March equinox show a significant differences, depending on whether the IMF field polarity is toward the Sun (“toward sector,” i.e., +Bx and −By) or away from the Sun (“away sector,” i.e., −Bx and +By). Densities in the toward sector near the March equinox increase before the sector boundary passes the Earth, with strong enhancements in the cusp region and the premidnight sector. Densities in the away sector near the March equinox decrease before the sector boundary passes the Earth, with a significant decrease in the early morning hours. On the other hand, near the September equinox, densities in the Southern Hemisphere do not show significant changes associated with the IMF sector polarity changes. The IMF By and the Bz offsets associated with the IMF sector polarity changes are related to specific behaviors in terms of thermospheric densities. In the toward (away) sector near the March equinox, IMF conditions that increase (decrease) the high-latitude southern thermospheric densities, the negative (positive) By and the negative (positive) Bz offsets, are maintained. On the other hand, in the toward (away) sector near the September equinox, the negative (positive) IMF By condition, which increases (decreases) the high-latitude southern thermospheric densities, and the positive (negative) IMF Bz offset condition, which decreases (increases) the high-latitude southern thermospheric densities, coexist.