The development and constant increase of antibiotic resistance has become a global health problem which is threatening the effective therapy of numerous infectious diseases. Understanding the mechanisms of resistance has a crucial impact on both choosing effective antibiotic treatment and design of new antimicrobial agents. The aim of this thesis was to assessed antimicrobial activity of amidine derivatives of 3,4-ethylenedioxytiophene in different anaerobic bacterial strains. These new chemical entities represent a novel class of antibacterial compounds, so called minor groove binders (MGBs). They inhibit DNA function and RNA sythesis in bacteria by binding to duplex DNA in the minor groove. Eight derivatives in total were tested by two different susceptibility testing methods – microdilution and agar dilution. The results of microdilution testing showed that two bis-phenyl derivatives with alkyl end groups (compounds 23 and 24) are the most active and have the best overall antibacterial activity. The other two bis-phenyl compounds (21 i 22), as well as other subclasses of derivatives, asimetrical compounds (10 i 11), bis-benzimidazole (19) and carboxamid-amidine (27) show, in general, lower antimicrobial activitiy compared to compounds 23 and 24. Agar dilution method revealed that compounds 22 – 24 have moderate activity on anaerobes (except Bacteroides and Lactobacillus strains which appeared insensitive). All bacterial strains are insensitive to remaining tested compounds. Since the results obtained by two different methods do not completely correlate, these findings should be critically revised and further investigations are recomended to explain the observed differences.