Due to the increasing number of respiratory diseases with developed inflammatory effects epidemics, the importance of finding a highly effective broad spectrum antiviral drug in combination with the anti-inflammatory activity is growing. Structurally similar derivatives of indolo[2,3-b]quinoxaline and indeno[1,2-b]quinoxalin-11-one exhibit a wide and partially similar spectrum of action, which makes them promising potential antiviral agents. These compounds were synthesized via substituted 1,2-diaminobenzenes and isatin (in case of 1) or ninhydrin (in case of 2) condensation and with no farther purification (indeno[quinoxalinone derivatives) or with washing with hot diluted alkali solution (to remove the major impurities of indoloquinoxaline derivatives). Thus, the aimed compounds were isolated as a mixture known, for a more detailed study of biological activity (especially in the case of ligandenzyme interactions), individual isomers should be investigated. This work is dedicated to the regio-isomeric composition investigation of synthesized indolo- and indenoquinoxalines and their separation. Considering minimal differences between isomeric compounds structure and chemical behavior, jnly chromatographic separation methods were required. Combination of poor solubility in low polar solvents and low separation effect for both of compound sets (indeno- and indoloquinoxalines) made column silica gel purification unacceptable. Indolo[2,3-b]quinoxaline isomers were separated by preparative TLC method using chloroform and ethyl-acetate as eluent. Separation was confirmed by UV-HPLC and MS-MS-UPLC methods. Indeno[1,2-b]quinoxalin-11-one derivatives were not separated in preparative quantities using silica gel column/thin layer methods.