Currently, the problem of selenium determination in various objects attracts a large number of scientists. Interest in this area is attributed to the biological importance of selenium, since it is both an important nutrient and has a toxic effect on the body, depending on its amount and the properties of the compounds in which it is contained. Checking the purity of selenium-containing organic compounds (both determination of impurities and analysis of the basic composition), which is carried out by methods of elemental analysis, is an important task, however, in modern literature there is lack of information regarding this problem. The purpose of the presented study is to develop a method for the determination of selenium in the basic composition of synthetic polyheteroatomic organic compounds by microwave plasma atomic emission spectrometry. Various selenodiazole derivatives were mainly used for analysis. Optimal conditions for sample preparation and atomic emission determination of the selenium content were specified. To mineralize the substances under study, oxygen flask combustion was used with the addition of potassium nitrate, which improves combustion and prevents the formation of soot. Hydrochloric acid at a concentration of 0.1 M was used as an absorption solution. It is noted that before measurements it is necessary to purge the monochromator and optimize the pressure in the atomic emission spectrometer nebulizer and optimize pressure in the atomizer. In addition, the number of replicates and sampling time were increased to optimize selenium measurement. Under specified conditions, the metrological characteristics of the technique were determined: the detection limit and quantitation limit, intra-laboratory precision and accuracy. Selenium was determined in 11 synthetic organic compounds with selenium content ranged from 12 to 51%. The error of the analysis did not exceed 0.3%, which meets the requirements of organic elemental analysis.