Abstract. True height electron density profiles observed with the Athens Digisonde were analyzed together with geomagnetic data indices for six magnetic storms in September and October 2000 in an effort to define the ionospheric structure during events of nighttime ionisation enhancements and to discuss the physical processes that may cause them. An upwelling of the F2-layer, limited to the dark hemisphere, was evident in all storm events as the ionospheric response to enhanced geomagnetic activity, but nighttime positive effects and nighttime height enhancements are attributed to two distinct mechanisms, according to our findings. Height enhancements are wave-like disturbances and the time delay of their occurrence at middle latitudes depends on the increase rate of the AE index, and consequently, on the rate that the solar wind input energy dissipates in the auroral ionosphere. Thus, they most probably originated in the auroral oval region and propagated toward the equator-like TID disturbances, with a periodicity that depends on the ionisation density. On the other hand, foF2 increases do not share the same wavy appearance, which could mean that they are not connected to TIDs and are not of auroral oval origin. The increased nighttime density can only be speculated to be due to increased downward fluxes from the plasmasphere.