The performed quantitative structure-mobility relationship (QSMR) study has investigated relative migration times of 11 guanidine/imidazoline derivatives, imidazoline receptor ligands, in CE system containing one of CDs, a-, beta-, or ?-CD, using linear and nonlinear modeling methods. The analyzed ligands and their inclusion complexes with CDs were fully examined and optimized at semiempirical parametrized model 3 level. The density functional theory, such as B3LYP/631G+(d,p)/321G(d)/STO-3G(d,p)/STO-3G(d), and ab initio theory, such as HF/321G(d)/STO-3G(d), were applied for molecular descriptors computation of the optimized ligands and their complexes. Predictive performances of the developed QSMR models were tested by use of the cross-validation and external test set prediction. Obtained results for Q2 values (0.869, 0.911, and 0.966 for CE system containing a-, beta-, and ?-CD, respectively) and root mean squared error of prediction (0.239, 0.242, and 0.288 for a-, beta-, and ?-CD, respectively) were proved high predictive power of the proposed models. Finally, multitarget QSMR model, using the ligands descriptors (X) and the relative migration time in presence of a-CD (Y1), beta-CD (Y2), and ?-CD (Y3), has been created. The multitarget QSMR model can be used as initial screening predictive tool for CE migration behavior of other related guanidine/imidazoline derivatives in presence of a-, beta-, and ?-CD.