Perfluorinated carboxylic acids (PFCAs) belong to anthropogenic fluoroorganic compounds that have been detected in the natural environment and living organisms including humans. A capillary zone electrophoretic method with indirect UV detection using 2,4-dinitrobenzoic acid (2,4-DNBA) as a chromophore probe has been developed for analysis of PFCAs (C6-C12) in water. Optimal analyte resolution and detection sensitivity was obtained with 50 mM Tris solution of pH 9.0 and 50% methanol as a background electrolyte (BGE). The baseline separation of C6-C12 PFCAs was obtained within 20 min with detection limits in the range from 0.6 to 2.4 ppm.