During geomagnetic storms different partial pressure gradients in the auroral ionosphere may result in H+, He+, O+ and molecular ions drifting with different velocities along the Earth’s magnetic field line. For relative drift velocities ⪡ 400 m s−1 it is shown that differential ion flows may be identified by two signatures in the autocorrelation function (ACF) measured by EISCAT. For larger relative drifts numerical simulations show that these signatures still exist and may result in an asymmetry in the incoherent scatter spectrum for O+ and molecular ions. It is demonstrated that UHF data can be reliably analysed for k2λD2 ≲ 1, but at high altitudes, where O+–H+ flows are expected, UHF observations will be restricted by large Debye lengths (k2λD2 > 1). Examples of ACFs based on polar wind theory are presented and discussed for the VHF system and finally it is shown that large ion temperature ratios (Ti(H+) >Ti(O+)) can significantly affect the velocity determination.