Objective: The aim of this study was to evaluate in vitro the antimicrobial efficacy of a modified 3-mix paste and to compare it with an iodoform paste (Ultrapex) against anaerobic microorganisms isolated from root canals of infected or necrotic primary teeth. Study design: An in vitro experimental assay was performed over isolated and identified anaerobic microorganisms of 21 samples, in order to compare the antimicrobial ability of both root canal filling materials, using a disc-diffusion method. Results: A total of 21 microbial samples (15 polymicrobial and 6 monomicrobial) were obtained, from which 19 different strains were identified. Modified 3-mix paste showed an excellent antimicrobial effect against most of both kinds of microbial samples, although some of them exhibited resistance; on the other hand, Ultrapex showed only minimal antimicrobial ability (null or low categories). Clostridium ramosum exhibited the most resistance to both materials. Conclusion: The bactericidal effect of the modified 3-mix paste was superior to Ultrapex, with a statistically significant difference, against anaerobic microorganisms isolated from infected root canals of primary teeth.