INTRODUCTION: The aim of this study was to compare the antimicrobial effects of MTAD, sodium hypochlorite (NaOCl) and their combination on endodontic micro-organisms. MATERIALS AND METHODS: Zone of Inhibition (ZI) and Minimum Inhibitory Concentration (MIC) were the techniques used. In ZI technique blood agar plates were inoculated with organisms, paper discs were soaked with irrigants and maximum zones of bacterial inhibition were recorded. In the MIC technique the irrigants were serially diluted in TSB tubes and 0.1 mL of the tested microbe solutions were added. Results were obtained on the basis of turbidity and growth on agar plates. Statistical analyses were carried out using ANOVA and Tukey tests. RESULTS: In ZI technique, we investigated 120 specimens including 5 microbial species, 3 irrigants and their control groups, each with 6 repetitions. The results demonstrated MTAD greater antimicrobial efficacy compared to NaOCl, and their mixture (M+N) against Staphylococcus (S) aureus, Enteric (E) bacteria and Enterococcus (E) faecalis (P<0.001). NaOCl was more effective in eradicating Candida (C) albicans than the others (P<0.01). MIC method (155 tubes) showed MTAD to be more effective against E. bacteria and S. aureus. MTAD and NaOCl were equally effective against E. faecalis; however, NaOCl was more effective against C. albicans. CONCLUSION: Bacterial species were more susceptible to MTAD than NaOCl, C. albicans, however, was more susceptible to NaOCl. The advantage of NaOCl is that it has broad spectrum antimicrobial activity. The joint solution (M+N) did not prove to be more effective than their individual use.