A simple, reliable and repeatable method, based on CE with amperometric detection has been developed for the simultaneous separation and determination of thyroxine (T(4)) and 3,3',5-triiodothyronine (T(3)). A carbon disk electrode was used as working electrode in this system and exhibited a good response at 1.05 V (versus Hg/Hg(2)Cl(2), 3 mol/L KCl) for two analytes. The CE separations were investigated in detail. At 21 kV of applied voltage, the two compounds were separated within 11 min in 0.05 mol/L Na(2)B(4)O(7)-NaOH buffer (pH 11.3). And the detection limits were as low as 1.0x10(-7) mol/L for T(4) and 8.5x10(-8) mol/L for T(3) (S/N=3), respectively. The proposed method was applied to analyze T(4) and T(3) in pharmaceutical formulations, and the results were satisfactory.