Aim:To compare the antimicrobial effects of two different irrigation solutions activated with erbium, chromium-doped yttrium, scandium, gallium and garnet (Er,Cr:YSGG) laser or an ultrasonic system and a photodynamic therapy (PDT) on Enterococcus faecalis (E. faecalis). Materials and methods: The root canals of 72 single-rooted human permanent incisors were prepared with ProTaper Universal rotary instruments and incubated with E. faecalis (ATCC 29212) for 4 weeks. Then the teeth were randomly divided into seven experimental groups with 10 specimens for canal disinfection procedures. Group I, standard needle irrigation (SNI) with 2.5% sodium hypochlorite (NaOCl); group II, SNI with 2% chlorhexidine gluconate (CHX); group III, laser-activated irrigation (LAI) by Er,Cr:YSGG of NaOCl; group IV, LAI of CHX; and group V, passive ultrasonic irrigation (PUI) of NaOCl; group VI, PUI of CHX; group VII, PDT. The remaining two teeth were used as the control group. After the disinfection procedures were completed, the root canals were filled with phosphate-buffered saline and bacterial samples were taken with sterile paper cones. The cultivation was performed on Mueller-Hinton agar (MHA) plates. The live bacteria were calculated by counting the colonies on these plaques. The statistical analysis was performed using Kruskal-Wallis H test and Miller's multiple comparison technique. Results: Both LAI and PUI of NaOCl and PUI of CHX were more successful than the PDT on root canal disinfection (p < 0.05). Conclusion: Within the limitation of the present study, the activation of NaOCl solution by Er,Cr:YSGG laser or an ultrasonic system can be useful in the elimination of the E. faecalis from the canal. The PUI of CHX also has similar results. Photodynamic therapy showed a lower performance compared to these methods. Clinical significance: The activation of the sodium hypochlorite with Er,Cr:YSGG laser or PUI may be useful for removal of the E. faecalis biofilm layer in the root canal.