Ionic liquids (ILs) are attractive stationary phases to broaden selectivity in gas chromatography (GC). The rational design, selection and application of ILs in comprehensive two-dimensional GC is a desirable goal. In this study, methods to predict two-dimensional chromatograms of fatty acid methyl esters (FAMEs) starting from given structures of IL stationary phases and their interactions with FAME solutes are described. Molecular parameters of the dipole moment, lowest unoccupied molecular orbital energy and molar volume of different ILs were calculated by using Gaussian 09. With established correlations between molecular simulation and linear solvation energy relationships, molecular parameters were converted to s, e and l values for stationary phase descriptors. This allowed reliable prediction of the equivalent chain length of FAMEs on each IL column (with the correlation R2=0.98). Isovolatility curves in GC×GC space of reference saturated FAMEs were then determined for each IL column to take into account the dependence of retention time on temperature in temperature-programmed separation. The resulting predicted GC×GC chromatograms were compared with previously reported experimental results. Correlations with R2 values of 0.99 and 0.98 were achieved for the first- and second-dimension retention times, respectively.