Background: Preservation of primary dentition is a must for orofacial development as it helps to maintain the eruption of permanent teeth, aids in mastication, and phonation. Objectives: The present study compares the antimicrobial activities of commonly used obturating materials for filling the root canals of primary teeth against the microorganisms commonly infect the roots. Methodology: the antimicrobial activities of four commonly used obturating materials, ZOE; Iodoform; Vitapex; and Endoflas, were evaluated by three methods; the first method was electron microscope images which detected the presence of the bacteria in dentinal tubules. The second method was CFU count method in which thirty extracted deciduous mandibular molars were incubated in a mixed-species suspension, obturated, cultured and the numbers of the bacterial colonies were reported for each obturated group. The third method was the agar diffusion method in which the antimicrobial activities of the obturating materials were tested against four microbial isolates (E. faecalis; E. coli; S. aureus and Ps. aeruginosa). Results: The four obturating materials reported different antimicrobial effect in CFU test which was not statistically significant; however, Endoflas and ZOE were superior to Vitapex and Iodoform. Bacterial resistances were detected against Vitapex and Iodoform. Conclusion: Obturating materials containing eugenol were more effective than other materials without eugenol.