The electrophoretic behaviour of neutral substances in non-aqueous capillary electrophoresis systems with tetraalkylammonium ions or long-chain trimethylammonium ions accompanied by different counter ions added have been investigated. Separation of neutral substances was only achieved in the highly dipolar aprotic solvents acetonitrile or propylene carbonate. The long-chain trimethylammonium ions were, however, not sufficiently soluble in acetonitrile. Thus, the studies comparing various types of ammonium ions were performed using propylene carbonate. The separation of the test solutes was improved with increasing concentrations of additives in the solvent. The type of ammonium ion as well as the counter ion were found to be important for the size of the separation window obtained. The separation principle was used for the determination of the water insoluble vitamin K1 as well as the preservatives methylparaben and propylparaben in a pharmaceutical product.