Ion flow along geomagnetic field lines is an important mechanism in the coupling of the magnetosphere-ionosphere system. Over the last 25 years or so, a wealth of satellite and radar observations has revealed the ionosphere as a steady and significant source of magnetospheric plasma. In the auroral ionosphere, field-aligned O+ upflows are often detected with fluxes exceeding those observed at higher altitudes, indicating that the ionosphere actively supplies ions to the magnetosphere. A number of mechanisms, principally associated with disturbed ionospheric conditions, have been proposed to account for ion upflows. This thesis documents a study of ion upflows observed in the auroral F-region and topside ionosphere. The work is based almost exclusively on incoherent scatter measurements from the EISCAT facility. More than 12 years' UHF Common Programme observations were employed in a study of the variation of upflow characteristics as a function of time, altitude, season and solar and geomagnetic activity. The study was extended in altitude with the inclusion of 5 years' vertical measurement from the EISCAT VHF radar. A quantitative comparison between upflow occurrence and plasma heating events was also performed. In addition, a case study is presented, examining three intervals of transient ion upflow detected during a run of the UK EISCAT Special Programme UFIS. The three events highlight some of the energization processes that can occur at different altitudes to generate field-aligned flow. Finally, a more detailed numerical investigation examined a day-side upflow observed by EISCAT in March, 1992. The event was modelled employing a simple 1-D approximation to the ion momentum-balance equation. The model explored the relative effects of plasma pressure, gravity and neutral wind on the field-parallel ion velocity; it was found that knowledge of the ion composition was necessary for accurate modelling of the observations.