New permethylated mono-6-deoxy-6-pyridin-1-ium and mono-6-deoxy-6-(1-vinyl-1H-imidazol-3-ium)-α- and -β-cyclodextrin trifluoromethanesulfonate ionic liquids were synthesized from the corresponding permethylated mono-6-hydroxycyclodextrins in a one-pot reaction and solvent-free procedure. Regioselective transformation of native α- and β-cyclodextrins with the use of a bulky tert-butyldiphenylsilyl protecting group afforded the desired 6-monosubstituted permethylated cyclodextrin derivatives in moderate yields. The new ionic liquids were tested as stationary phases in capillary GC columns towards chiral discrimination in enantio-GC analysis of racemic mixtures. The permethylated 6-deoxy-6-pyridin-1-ium-α-cyclodextrin trifluoromethanesulfonate displayed good enantiomeric separations for some racemic esters and lactones, as well as epoxides. In particular, for both the racemic whiskey lactone and the high boiling point menthyl laurate, not successfully separated in a commercial cyclodextrin phase, the enantiomeric separations were achieved isothermally at 140 °C.