Chronic periodontitis (CP) is an infectious disease resulting in inflammation of the supporting structures of the teeth, progressive loss of bone loss and insertion. The aim of this study is to evaluate the effects of antimicrobial Photodynamic Therapy (aPDT) as adjuvant to periodontal surgery treatment (PST) in patients diagnosed with generalized severe chronic periodontitis (GSCP). Twenty patients with a clinical diagnosis of CP will be treated in a split-mouth design study to either aPDT associated with surgical access for scaling and root planning (SASRP) or SASRP 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 only one episodes. All patients will be monitored for 30 and 90 days after PST. 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 PST. Subgingival plaque samples will be collected (at baseline and 30 and 90 days after the PST) and the counts of 40 subgingival species will be determined using DNA-DNA checkerboard hybridization. Data obtained will be statistically analyzed.