Lithium ions in LiFePO4 were observed directly at atomic resolution by an aberration-corrected annular-bright-field scanning transmission electron microscopy technique. In addition, it was found in partially delithiated LiFePO4 that the remaining lithium ions preferably occupy every second layer, along the b axis, analogously to the staging phenomenon observed in some layered intercalation compounds. This new finding challenges previously proposed LiFePO4/FePO4 two-phase separation mechanisms.