Statement of Problem: The main purpose of a root canal treatment is to eliminate the bacteria and their products from the pulp space. Sodium hypochlorite has excellent antibacterial properties, but also some negative features.Purpose: The aim of the present study is to compare the antimicrobial effect of Aloe Vera solution with sodium hypochlorite on E.faecalis in the root canals of human extracted teeth.Materials and Method: Sixty human extracted single rooted teeth were selected for this in vitro study. The teeth recruited in this study had no cracks, internal resorption, external resorption and calcification. Enterococcus faecalis was injected in the root canals of all teeth. The teeth were then divided into three groups randomly. Each group consisted of 20 teeth that were all rinsed with one of the following solutions: sodium hypochlorite 2.5%, Aloe vera and normal saline. Subsequent to rinsing, root canals of all teeth were sampled. The samples were cultured and growth of the bacteria was assessed after 48 hours. The number of colonies of the bacteria was then counted.Results: The difference between the inhibitory effect of Aloe vera and normal saline on E.faecalis was not significant according to independent t-test (p= 0.966). The inhibitory effect of sodium hypochlorite on E.faecalis was much greater than that of Aloe vera and normal saline (p< 0.001).Conclusion: Aloe vera solution is not recommended as a root canal irrigator, but future studies are suggested to investigate the antibacterial effect of Aloe vera with longer duration of exposure and as an intra canal medicament.