Cell tracking by in vivo magnetic resonance imaging (MRI) requires strategies of labelling the cells with MRI contrast agents. The principal routes to achieve efficient cell labelling for neurological applications are discussed with methodological advantages and caveats. Beyond temporo-spatial localization of labelled cells, the investigation of functional cell status is of great interest to allow studies of functional cell dynamics. The two major approaches to reach this goal, use of responsive contrast agents and generation of transgenic cell lines, are discussed.