Objective: The present study aimed to evaluate and compare six different materials commonly used for filling the root canals of primary teeth for antimicrobial efficacy against some of the microorganisms commonly found in infected root canals. Study design: In this experimental in vitro study six root canal filling materials were tested for antimicrobial efficacy against eight microbial strains using the agar diffusion method. Results: Zinc oxide eugenol paste exhibited the strongest antimicrobial potential followed by Endoflas™, zinc oxide-calcium hydroxide-sodium fluoride mixture, zinc oxide-calcium hydroxide mixture and calcium hydroxide paste (Apexcal™). The addition of sodium fluoride to the zinc oxide-calcium hydroxide mixture enhanced the antimicrobial efficacy. Metapex™ demonstrated minimal inhibition and Vaseline™ was non-inhibitory. Conclusions: All the test filling materials demonstrated varying antimicrobial activity against the microorganisms tested. Zinc oxide eugenol paste and materials containing zinc oxide were found to be more effective against the microorganisms compared to materials without zinc oxide.