Researches with nitro compounds mainly relates to the synthesis of their derivatives used as unusual intermediate compounds. Because of their high reactivity in SNvin reactions, polyhalo-nitro-butadienes have been shown in many studies to have many properties as well as medical and pharmaceutical effects such as antitumor, bactericidal, fungicide and algicide. This study deals with the design, characterization of structures and the discovery of their antibacterial and antifungal properties based on new (E)-S- and (E)-N,S-polyhalonitrobutadiene analogues possessing piperazine, piperidine and morpholine groups. The antibacterial and antifungal activity of synthesized S- and N,S-substituted perhalo-nitro-butadienes were evaluated against to Escherichia coli B-906, Staphylococcus aureus 209-P, Mycobacterium luteum B-917 for bacteria and Candida tenuis VKM Y-70, Aspergillus niger F-1119 for fungi. Antimicrobial activity of the synthesized compounds was determined by using the diffusion method and serial dilution method. Compounds 2-Nitro-1,3,4,4-tetrachloro-1-hexylsulfanyl-1,3-butadiene and (E)-2,6-dimethyl-4-(3,4,4-trichloro-2-nitro-1-(octylthio)buta-1,3-dien-1-yl)morpholine with high antibacterial effect against strains E. coli and M. luteum and the derivative (E)-1-benzhydryl-4-(3,4,4-trichloro-1-(hexylthio)-2-nitrobuta-1,3-dien-1-yl)piperazine with antifungal agent against test-cultures A. niger and C. tenuis at MIC 1.9 µg/mL were identified as the most potent. Synopsis This study deals with the characterization of structures and the discovery of their antibacterial and antifungal properties based on new (E)-N,S-polyhalonitrobutadiene analogues. 1b and 7 with high antibacterial effect against strains E. coli and M. luteum. 9 with antifungal agent against test-cultures A. niger, C. tenuis at MIC 1.9 µg/mL were identified as the most potent.