Purpose: To evaluate the antimicrobial effect of chitosan as root canal irrigant on Enterococcus faecalis in comparison to 3%NaOCL in experimentally infected primary anterior root canals. Materials and methods: Access cavity and mechanical preparation of root canals of 30 extracted primary anterior teeth which were then sterilized at autoclave at 1210 for 15 minutes. These teeth inoculated with Enterococcus faecalis with reference strain ATCC 19433.Then grouped into three groups which were irrigated with 3%NaOCl, 0.5% chitosan and saline respectively. Samples were cultured on bile auscline agar incubated at 370 for 24 hours. Counting of colony forming units formed before and after irrigation was performed. Results: Chitosan had higher antimicrobial effect than saline and lower than NaOCl. Statistical analysis between the groups revealed that there was a statistically significant difference between the three irrigants (P-value = 0.001). Conclusion: Chitosan solution can be used as a natural alternative to sodium hypochlorite in root canal irrigation, but may need to increase its concentration or the time of application inside the root canals and also should be supported by in vivo studies.