A selective MEKC method was developed for the analysis of didanosine in bulk samples. Successful separation of didanosine from 13 of its potential impurities, derived from the various synthetic preparation procedures, was achieved. As CZE gave poor separation selectivity, MEKC was preferable. The use of EKC allowed achievement of the separation in a significantly shorter time than conventional HPLC. An anionic long-chain surfactant, lithium dodecyl sulfate (LiDS), was used as the pseudostationary phase and sodium tetraborate buffer as the aqueous phase. In order to obtain the optimal conditions and to test the method robustness, a central composite response surface modeling experiment was performed. The optimized electrophoretic conditions include the use of an uncoated fused-silica capillary with a total length of 40 cm and an ID of 50 microm, a BGE containing 40 mM sodium tetraborate and 110 mM LiDS at pH 8.0, an applied voltage of 18.0 kV, and the capillary temperature maintained at 15 degrees C. The method was found to be robust. The parameters for validation such as linearity, precision, and sensitivity are also reported. Three commercial bulk samples were analyzed with this system.