In this study it is shown that the chromate background electrolyte suggested early by the authors is suitable for the determination of chlorate and perchlorate ions in drinking water using capillary electrophoresis. The analysis conditions were found allowing one to determine the ions with concentration lower 0.5 of maximum permissible values. The calibration curves were linear within the range of 0.01-0.1 mM with sample injection at pressure of 50 mbar for 100 s. The method validity was proved check by the method by the standard addition method. Using the developed method the real samples of drinking water of Krasnoyarsk were analyzed. Chlorate and perchlorate ions were not found in the sample studied.