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This study tested the effect of photodynamic antimicrobial chemotherapy (PACT) on single-species biofilm grown in a flow-cell system using methylene blue associated with nanoparticles of β-cyclodextrin and light sources of red laser or light-emitting diode (LED). The flow-cell system comprised chambers for biofilm cultivation with S. mutans under continuous hydrodynamic conditions containing BHI supplemented with 1% sucrose (w/v). Biofilms were divided into six groups (n = 6): C (control), P (photosensitizer + β-cyclodextrin), L (laser), LED (light-emitting diode), LP (laser + photosensitizer + β-cyclodextrin), and LEDP (LED + photosensitizer + β-cyclodextrin). Groups irradiated with laser were exposed to a low power light (λ = 660 nm, 320 J/cm2, 0.1 W, 9 J, 90 s). Groups irradiated with LEDs were exposed to 12 LEDs (λ = 660 nm, 8.1 J/cm2, 0.09 W/cm2, and 8.1 J for 90 s). The antibacterial potential of treatments was assessed by viable S. mutans counts of biofilm in selective medium. The vitality of intact biofilms was qualitatively evaluated by confocal laser scanning microscopy analysis (CLSM). The data were analyzed by Welch’s one-way ANOVA followed by Scheffe´s post-hoc tests (p 0.05). The number of S. mutans was significantly reduced in LP and LEDP groups (p |