The separation of natural mixtures of free fatty acids, their methyl esters and triacylglycerols (TAGs) was studied by applying the reversed-phase capillary electrochromatography (CEC) and HPLC. Home-made CEC instrumental setup, as well as the preparation method of microcolumns (200 mm bed length, 100 mum I.D., Hypersil ODS packing, d(p) = 3 mum) have been proposed. The retention time reproducibility obtained at the voltages of 10 and 15 kV was 0.95% and 1.7%, respectively. Relative retention times of individual TAGs were compared using HPLC or CEC columns of identical packings. The obtained results have shown that the selectivity of the separation in non aqueous reversed phase systems (NARP) by CEC and HPLC techniques are very similar or almost identical, and are independent of the number of double bonds or carbon atoms in TAG molecules. The ionic strength of the mobile phase significantly influenced the reduced plate height (h) of the columns. In NARP-CEC, h-was improved significantly with an increase in the ammonium acetate concentration in the mobile phase up to 50 mmol L-1 (the composition of the mobile phase was: acetonitrile/propanol-2/n-hexane, 61:24:15 v/v). In NARP-HPLC such an effect was not observed. It is expected that the improvement of the detection mode and the microcolumn packing in the NARP-CEC will make this technique more powerful towards the separation of TAGs than the commonly used HPLC method is.