The treatment of aggressive periodontitis (AgP) represents a challenge for clinicians, because there are no standardized protocols for efficient control of the disease. The aim of this study is to evaluate the effect of multiple applications of antimicrobial photodynamic therapy (aPDT) as an adjunct to non-surgical periodontal treatment (nsPT) in patients diagnosed with AgP. Twenty patients with a clinical diagnosis of AgP will be treated in a split-mouth design study to either aPDT associated with scaling and root planning (SRP) or SRP only. aPDT will be performed by using a laser light source with 690 nm wavelength associated with a phenothiazine photosensitizer. The applications will occur in four episodes (days 0, 2, 7 and 14). All patients will be monitored for 90 days. Clinical assessment of plaque index, probing depth, clinical attachment level and bleeding on probing will be performed at baseline (pre-intervention period) and 30 and 90 days after the nsPT. Subgingival plaque samples will be collected (at baseline and 30 and 90 days after the nsPT) and the counts of 40 subgingival species will be determined using DNA-DNA checkerboard hybridization. Gingival crevicular fluid samples will be collected (at baseline and 14, 30 and 90 after the nsTP) for evaluation the volume of fluid (Periotron) and the levels of Interleukin 1 beta, Interleukin 10 and Tumor Necrosis Factor alpha (Luminex). Data obtained will be statistically analyzed.