Ionic liquids, though promoted as green solvents, exhibit significant toxicity against various organisms in the ecosystem. The lipophilicity of cations plays a determining role in this toxicity. The experimental lipophilicity values being available for a limited number of cations, we modeled the chromatographically derived lipophilicity parameter logk0 of ionic liquid cations using Extended Topochemical Atom (ETA) descriptors and Quantum Topological Molecular Similarity (QTMS) descriptors. Both types of descriptor were previously found to be important inmodeling selected toxicity endpoints of ionic liquids.We have performed both internal and external validation tests and randomization experiments while developing the models. The present study suggests that the ETA and QTMS descriptors are efficient in developing robust and reliable lipophilicity models for cations of ionic liquids. The developed models show that lipophilicity increases with the size of cations, and decreases with their electron-richness and hydrogen bonding propensity. The electronic character of the bond joining the quaternary atom with sp3 hybridized carbon is also important. The computed lipophilicity obtained from the developed model was also applied to the computation of rat toxicity data of a large number of compounds, and gave highly satisfactory results.