The main cause for endodontics treatment failure is microorganisms remaining in place. Entrococcus faecalis is one the most resistant bacteria in endodontic failures. Based on these facts we decided to compare the antibacterial effects of erbium, chromium-doped yttrium, scandium, gallium and garnet (Er,Cr:YSGG) laser and chlorhexidine 2% solution against E. faecalis. In this experimental study, 60 anterior teeth were divided into four groups: chlorhexidine (n = 25), Er,Cr:YSGG laser (2780 nm, 25 mJ, 0.5 W) (n = 25), positive and negative control (n = 5). About 56% of laser group plates and 4% of chlorhexidine plates showed bacterial growth. Chlorhexidine 2% was significantly more effective against entrococcus than Er,Cr:YSGG laser (p < 0.001). Both Er,Cr:YSGG laser and chlorhexidine 2% had bactericidal effect on E. faecalis, however chlorhexidine 2% was significantly more effective.