The potentialities of new ionic liquids (ILs) based on choline were evaluated as an electrophoretic medium in capillary electrophoresis for the analysis of alkaline and alkaline earth cations (Li(+), K(+), Na(+), Cs(+), Mg(2+), Ba(2+), Ca(2+), and Sr(2+)) with indirect UV detection. Two types of capillaries were tested: an untreated fused silica and fused silica coated with a film of polyvinylalcohol. The coated capillary proved to be the best adapted for the metal ions studied. Moreover, it appeared that the nature of the ionic liquid anion influenced the baseline stability, and the bis(trifluoromethylsulfonyl) imide (NTf(2) (-)) anion seemed to be the most efficient. These preliminary studies led us to synthesize a new ionic liquid, 2-hydroxy-N,N,N-trimethyl-1-phenylethanaminium NTf(2) (phenylcholine NTf(2)). This liquid was able to act as the running electrolyte and probe, generating the background signal in indirect UV light and consequently simplifying the electrophoretic medium. Excellent baseline stability, good reproducibility, as well as good sensitivity of detection were obtained with this new ionic liquid. Thus, 510,000 plates/meter for Li(+) with 40 mM IL were successfully obtained. The optimal concentration of IL was 20 mM with a detection limit ranging from 28 microg L(-1) for Li(+) to 1,000 microg L(-1) for Cs(+). This method (phenylcholine NTf(2) with polyvinylalcohol capillary) was applied to analyze different commercial source and mineral waters. Finally, the potentiality of this ionic liquid in nonaqueous capillary electrophoresis was explored. The use of phenylcholine NTf(2) with a fused silica capillary, in pure methanol medium and in the presence of acetic acid, made it possible to obtain separation selectivity different from that obtained in aqueous medium.