A micellar electrokinetic capillary chromatography was performed at 25°C and 30 kV (under pressure of 15 mbar), with 30 mM borate buffer (pH 9.0), 60 mM sodium dodecysulfate, and 10% (v/v) ethanol as background electrolyte for the determination of sulfamethoxazole and trimethoprim. UV detection was at 205 nm. Recoveries were optimal and acceptable after extraction with ethanol / deionized water (1:1, v/v) for both investigated compounds from laboratory mixtures of standards. The method was shown to be specific, accurate (recoveries were 99.9 ± 0.4% for sulfamethoxazole and 99.8 ± 0.3% for trimethoprim), linear over the tested ranges (correlation coefficients ≥ 0.9990) and precise (RSD below 0.6%). The method was applied to determine sulfamethoxazole and trimethoprim in tablets, powder for cutaneous use and solution for infusion.