Micellar electrokinetic capillary chromatography (MECC) has been developed as an efficient method for the determination of the thiocyanate ion, iodide, nitrite and nitrate. The use of various alkyltrimethylammonium ions was found advantageous for MECC compared to negatively charged surfactants, as this resulted in low migration times for the anions and thereby fast analysis. Moreover, the MECC system, using positively charged surfactants (dodecyltrimethylammonium bromide, DTAB), was effective in separating the anions of interest from interfering organic anions present in extracts from biological samples such as milk and blood. Detection of the anions was performed by direct UV. The performance of the developed method was satisfying; however, a low number of theoretical plates for the thiocyanate ion indicated the need for some improvements in this respect. The sensitivity of the method increased with a factor two by using a 75 μm I.D. capillary instead of the 50μm I.D. capillary, whereas use of a high-sensitivity optical cell assembly increased the sensitivity an additional nine times. Repeatability with the 50-μm capillary was satisfying with respect to migration time, relative migration time and normalised peak area (except for the thiocynate ion) of the anions, with relative standard deviations varying between 0.24 and 0.29%, 0.07 and 0.16%, and 1.75 and 2.37%, respectively, whereas some improvements are still needed for the normalised and relative normalised peak areas for the thiocyanate ion (13.50 and 13.91%). Apart from the thiocyanate ion ( r 2 = 0.9748), linearity studies gave correlation coefficients between 0.9962 and 0.9975 for the normalised peak areas.