Capillary zone electrophoresis (CZE) was used for the pKa determination of several acidic drugs. The methodology relies on the measurement of the effective mobility of ionic species in electrophoretic buffers prepared at different pH values. The validation of the assay was achieved by comparing the pKa obtained by CZE with literature values obtained by standard techniques for a variety of soluble drugs (sulphadimethoxine, tolbutamide, nitrofurantoin, sulphaphenazole, ibuprofen, hexobarbitone) whose pKa values ranged from 4 to 8. The pKa values determined by CZE correlated with literature values (slope of 0.99 and coefficient of correlation of 0·995 as determined by linear regression). The main advantage of the CZE methodology over conventional techniques was the low amount of material needed (∼1 mg to prepare a stock solution) and the low concentration required (50–100 μm in this work) for pKa determination. Using eight non-steroidal anti-inflammatory drug candidates as model compounds, we were able to determine the pKa of these sparingly soluble compounds in 100% aqueous solutions. The values obtained by CZE for these compounds were compared with the apparent pKa values obtained by potentiometry in 50% methanolic solutions. Using this latter technique, three of the eight compounds tested could not have their pKa determined because of precipitation problems. The pKa values of the five remaining compounds determined by potentiometry were consistent with those determined by CZE. This work has shown that CZE can be a powerful automated technique for pKa determination and one of its major advantages is its application to the pKa analysis of sparingly soluble compounds.