BACKGROUND The treatment of aggressive periodontitis has always presented a challenge for clinicians, but there are no established protocols and guidelines for the efficient control of the disease. METHODS Ten patients with a clinical diagnosis of aggressive periodontitis were treated in a split-mouth design study to either photodynamic therapy (PDT) using a laser source with a wavelength of 690 nm associated with a phenothiazine photosensitizer or scaling and root planing (SRP) with hand instruments. Clinical assessment of plaque index (PI), gingival index (GI), bleeding on probing (BOP), probing depth (PD), gingival recession (GR), and relative clinical attachment level (RCAL) were made at baseline and 3 months after treatment with an automated periodontal probe. RESULTS Initially, the PI was 1.0 +/- 0.5 in both groups. At the 3-month evaluation, the plaque scores were reduced and remained low throughout the study. A significant reduction of GI and BOP occurred in both groups after 3 months (P <0.05). The mean PD decreased in the PDT group from 4.92 +/- 1.61 mm at baseline to 3.49 +/- 0.98 mm after 3 months (P <0.05) and in SRP group from 4.92 +/- 1.14 mm at baseline to 3.98 +/- 1.76 mm after 3 months (P <0.05). The mean RCAL decreased in the PDT group from 9.93 +/- 2.10 mm at baseline to 8.74 +/- 2.12 mm after 3 months (P <0.05), and in the SRP group, from 10.53 +/- 2.30 mm at baseline to 9.01 +/- 3.05 mm after 3 months. CONCLUSIONS PDT and SRP showed similar clinical results in the non-surgical treatment of aggressive periodontitis.