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The aim of the present study was to evaluate the potential of minimally invasive periodontal treatment using repeated photo-activated oral disinfection (PAD) with red light emitting diodes as an adjunct to ultrasonic scaling (US) in the treatment of chronic periodontitis. In a single-centred, randomized clinical trial involved 40 patients with untreated chronic periodontitis received US with repeated 3 episodes of PAD (test group) or US alone (control group). Clinical parameters (plaque index (PI), bleeding on probing (BOP), probing pocket depth (PPD), clinical attachment level (CAL)) were recorded for 12 months and subgingival biofilm analyses for five periodontal pathogens (A. actinomycetemcomitans (Aa), P. gingivalis (Pg), P. intermedia (Pi), T. forsythia (Tf), T. denticola (Td)) were performed for 6 months. Supportive periodontal treatment (SPT) was repeated every 3 months during the clinical trial, additional one episode of PAD was also applied in the test group. Both treatment modalities improved clinical parameters after 3 months and SPT maintained favourable clinical outcomes during 12 months. There were no statistical significant differences between the treatment groups. Statistical significant reduction of Aa, Pg, Tf, Td (p<0.05) was observed in the test group. In moderate pockets significant reduction of Pg, Tf, Td (p<0.05) and in deep periodontal pockets reduction of Pg, Pi, Td (p<0.05) was observed. Within the limits of the present study it may be concluded that the addition of PAD to US significantly reduced some key periodontal pathogens, however, patients with a history of periodontitis should be on SPT every 3-4 months.