The work is devoted to the selection of optimal conditions for electrophoretic determination of heterocyclic thioamides which showed chemical activity to molecular iodine. It gives a reason to believe that the thioamides can be considered in the future as the basis for the development of antithyroid drugs. Due to the high sensitivity, the method of СE is versatile and successfully applied in toxicology and for monitoring pharmaceuticals in body fluids and tissues. The developed CE-technique of determination of 2-thioxo-5-(3,4,5-trimethoxybenzylidene) thiazolidin-4-one (I), 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt (II) and 4-amino-5-(furan-2-yl)-4H-1,2,4-triazole-3-thione (III) by aqueous capillary electrophoresis allows to estimate the content of compounds in the range of 3.10-25 µg/mL for (I), 2.64-159 µg/mL for (II) and 1.45-12.80 µg/mL for (III). The technique was tested in analysis of urine. Selected conditions of the liquid-phase extraction are suitable for determination of compounds (II) and (III) in the urine. The optimal conditions of liquid-phase extraction which allow to extract approximately 74-97% of studied compounds were determined.