The aim of this study was to evaluate the antimicrobial efficacy of propolis when used as an intracanal medicament against Candida albicans ATCC 10231 (C. albicans) and Enterococcus faecalis ATCC 51299 (E. faecalis) and compare this efficacy to that of Chlorhexidine digluconate (CHX). Methods: This study utilised 70 freshly extracted single rooted human teeth. The crowns were sectioned at the cemento-enamel junction and the root lengths were standardized to 15-17mm. After root canal preparation and sterilization, the canals were contaminated with a mixture of suspension containing C. albicans ATCC 10231 and E. faecalis ATCC 51299. Teeth were randomly divided into 3 groups including one control group. The canals were then filled with intracanal medicament, sealed coronally and incubated at 37 degree celsius for an experimental time period of 48 hrs and 10 days. Microbiological sampling was carried out at the end of 48 hrs and 10th day to determine the Colony Forming Units per ml (CFU/ml). Statistical Analysis used: One way Analyses of Variance and post hoc test of Least Square Distance were used to assess the statistical significance between groups. In the above test p value less than 0.05 was taken to be statistically significant. The data was analyzed using Statistical Package for Social Science (SPSS, V 10.5). Results: When the activity against E. faecalis ATCC 51299 was evaluated, Ethanolic extract of propolis (Group 2) was significantly more effective than CHX (Group 1) for both the experimental time periods. Ethanolic extract of propolis (Group 2) was less effective than CHX (Group 1) at the end of 48 hrs against C. albicans ATCC 10231 and this difference was statistically significant. At the end of 10 days this difference was not significant. Conclusion: Ethanolic extract of propolis is effective as an intracanal medicament ex vivo.