Treatment outcome of endodontic perforations depends on successful elimination of the associated microorganisms and infected tissues as well as the effective seal of the root-end or perforation site to prevent future contamination. Ideally, perforation repair material has to be bacteriostatic or bactericidal in order to prevent bacterial contamination as well as good sealing properties and biocompatibility. The aim of this study was to evaluate the antimicrobial effects of BioAggregate (BA) and Mineral Trioxide Aggregate (MTA) on the standard strains of Candida albicans, Enterococcus faecalis, Escherichia coli, Streptococcus mutans, Streptococcus sanguinis and Pseudomonas aeruginosa using the agar disc diffusion test. Colonies of each strains were harvested from the medium and microorganisms were diluted to obtain a suspension of approximately 108 cfu/ml. Petri plates with blood agar base with 5% sheep blood or Sabouraud dextrose agar (for C.albicans) were inoculated with experimental suspensions and BA and MTA discs prepared as 2 mm length and 6 mm diameter were placed. After 24 and 48 hours incubation, the diameters of the zones of inhibition were measured. The results of the disc diffusion tests showed that BA and MTA were effective on the tested microorganisms at 24 and 48 hours incubation periods. BA and MTA showed similar antimicrobial effects on C.albicans and E.coli. BA was more effective than MTA on S.mutans, E.faecalis and P.aeruginosa, however MTA was more effective than BA on S.sanguinis at 48 hours. When the time efficiency of the materials were compared, there was no statistically difference between 24 to 48 hours on E.coli, E.faecalis, S.mutans, S.sanguinis in both two groups (p> 0.05). There was statistically significant decrease 24 to 48 hours on C.albicans in BA and MTA groups and P.aeruginosa in BA group (p< 0.05). It can be concluded that although BA and MTA displayed similar antimicrobial efficacy on the tested microorganisms newly improved material BA demonstrated superior antimicrobial activity than other.