Objective: The present study aimed to evaluate and compare some filling materials used for filling the root canals of primary teeth for antimicrobial efficacy against some of the microorganisms commonly found in infected root canals. Materials and Methods: The antbacterial activities of obturating materials, Endoflas, Iodoform, ZOE; Vitapex was done by two methods. The first was the agar diffusion method in which the filling materials were tested against four microbial isolates (Ps. Aeruginosa, E. coli; E. faecalis; E. coli and S. aureus). Second was, CFU count in which thirty extracted primary mandibular molars roots were incubated in mixed-species suspension, obturated, cultured and the CFU were reported for each filling material. The data were collected and statistically analyzed using ANOVA and Kruskil Wallis tests. Results: The results of this study showed statistically significant difference between all the obturating materials and the antimicrobial effect of Endoflaswas superior to ZOE, Vitapex and Iodoform against all microorganisms were tested. While in roots specimens test there was no statistically significant difference between groups. Conclusion: The tested obturating materials demonstrated varying antimicrobial efficacy against the microorganisms tested. Endoflas paste and material containing eugenol were found to be more effective against the microorganisms compared to materials without eugenol.