Introduction:Pericoronitis is a common disease in the eruption phase of third molars, sometimes debilitating, with an impact on the quality of life. The most indicated treatment in the initial phase is the irrigation for cleanliness of the region. In order to reduce the chances of systemic dissemination of the infection and antibiotics use, it is mandatory to test effective treatments in the initial phase of pericoronitis avoiding the evolution of the infectious disease. Photodynamic therapy (PDT) is an interesting alternative because it is an effective antimicrobial treatment that is easy to perform and does not select bacterial resistance. The methylene blue (MB) used in PDT has been studied in an oral formulation, which optimizes the formation of monomers increasing its antimicrobial action.Objective:The aim of this study is to evaluate the effectiveness of PDT with MB in an astringent vehicle in pericoronitis on the initial phase in healthy patients through microbiological, clinical, and immune response. The impact of pericoronitis on oral health-related quality of life (OHRQoL) of these patients will also be evaluated.Method:In this randomized, controlled, double-blind clinical bioequivalence protocol, 64 healthy patients with pericoronitis will be evaluated. Patients will be randomized into the positive control group (G1) (n = 32): irrigation with sterile saline and PDT (conventional MB at 0.005% concentration and irradiation with low intensity laser λ = 660 nm, 9J per point and radiant exposure of 318 J/cm2), and the experimental group (G2) (n = 32): treatment identical to G1, however, MB will be delivered in a new formulation for oral use. Microbiological analysis will be performed by RT-PCR for the bacterium Tannerella forsythia. Gingival crevicular fluid and saliva will be collected to evaluate cytokines by Luminex assay (Luminex Corporation, Austin, TX). The pain (visual analogue scale), swelling and buccal opening (digital caliper), and OHRQoL will also be evaluated through the OHIP-14 questionnaire. The variables will be evaluated in T1 (baseline), T2 (immediately after PDT), and T3 (4th day after PDT). Registration: clinicaltrials.gov NCT 03576105. Registered in July 2018.