We investigated the effectiveness of chlorine dioxide (ClO2) solution in comparison to sodium hypochlorite (NaOCl) and chlorhexidine gluconate (CHX) in the elimination of intracanal Enterococcus faecalis biofilm. Extracted human teeth were inoculated with E. faecalis. After preparation the canals were irrigated with ClO2, NaOCl, CHX or physiologic saline for control. Two and five days later bacterial samples were collected and streaked onto Columbia agar. CFU/mL were counted. The canal walls were investigated by scanning electron microscopy (SEM). The gas phase was investigated in an upside down Petri dish where E. faecalis was inoculated onto blood agar. The irrigants were placed on absorbent paper into the cover. Bacteria were detectable in the control group, but not in any of the irrigants groups. There was a massive reinfection 2 or 5 days after irrigation in the control group. The lowest reinfection was found after the ClO2 treatment. These findings were confirmed by SEM images. We observed an antibacterial effect of ClO2 and NaOCl gas phases on E. faecalis growth, but not of CHX. ClO2 eliminates intracanal biofilm and keeps canal nearly free from bacteria. We suggest the use of high purity ClO2 as a root canal irrigant in clinical practice.