A new capillary electrophoresis method with field-amplified sample stacking (FASS) was developed for the analysis of sulfadiazine and sulfamethoxazole. After optimization of the separation and concentration conditions, the two compounds can be separated within 7 min and quantified with high sensitivity, with detection limits of 0.48 ng/mL for sulfadiazine and 0.76 ng/mL for sulfamethoxazole. This resulted in a 300-1500-fold improvement in concentration sensitivity relative to conventional capillary electrophoresis methods. The method was useful for qualitative and quantitative analysis of sulfadiazine and sulfamethoxazole in their preparations with recovery of 99.0%-102% for sulfadiazine and 99.5% - 99.7% for sulfamethoxazole.