A drift-kinetic theory for ion phase-space vortices in magnetized plasmas is developed, taking into account the effects of the ion polarization and anisotropic heating by ion beams. It provides a theoretical explanation for the bipolar electrostatic structures in the auroral zone of the Earth's magnetosphere and their spatial and temporal scales, as observed by S3-3, Viking, FREJA, Polar, and FAST spacecrafts. Several types of quasi-three-dimensional ion holes are obtained analytically, in the form of either cylinders or ellipsoids. Although topologically different, they produce similar signals on the spacecraft and cannot be distinguished on the basis of the existing satellite data.