This study aimed to evaluate the antibacterial action of KTP (potassium-titanyl-phosphate) laser irradiations (compared with 980 nm diode laser), associated with conventional endodontic procedures, on Enterococcus faecalis biofilms. Fifty-six dental roots with single canals were prepared with Ni-Ti rotary instruments, autoclaved, inoculated with an E. faecalis suspension and incubated for 72 h. They were randomly allocated to control and treatment groups. Laser parameters were as follows: power 2.5 W, Ton 35 ms, Toff 50 ms (KTP laser); power 2.5 W, Ton 30 ms, Toff 30 ms (980 nm diode laser). To evaluate the residual bacterial load, BioTimer Assay was employed. The chemo-mechanical treatment together with laser irradiations (KTP and 980 nm diode lasers) achieved a considerable reduction of bacterial load (higher than 96% and 93%, respectively). Regarding both laser systems, comparisons with conventional endodontic procedures (mortality rate of about 67%) revealed statistically highly significant differences (P ≤ 0.01). This study confirms that laser systems can provide an additional aid in endodontic disinfection.