Chronic periodontitis is a result of polymicrobial infection and its treatment aims removal of dental calculus and biofi lm from the periodontal pocket. Many hand and power-driven instruments are created for this purpose. In recent years, lasers are widely discussed tools for periodontal therapy. The aim of the present study is to evaluate the early microbiological and clinical effectiveness of the Er:YAG laser in the treatment of chronic periodontitis. 30 patients with moderate chronic periodontitis were enrolled in the study. Using a split-mouth design they were treated either with Er:YAG laser (chisel tip, 100 mJ, 15 Hz, 5-6 water spray)-test group or with Gracey curettes- control group. Probing pocket depth (PPD), gingival recession (GR), clinical attachment level (CAL), bleeding on probing and plaque presence were evaluated at baseline and one month after the therapy. Microbiological samples were taken from the deepest four pockets of each quadrant from 20 randomly selected patients (n = 80). They were evaluated using real time PCR for periodontal pathogens from the red complex (Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia). One month after therapy in the control group PPD decreased from 4.59 mm to 3.36 mm, the CAL gain was 1.09 mm and the reduction of bleeding and plaque - from 87.9% to 33.7% and from 75.9% to 40.9%, respectively. In the test group PPD decreased from 4.58 mm to 3.15 mm, the CAL gain was 1.37mm and the reduction of bleeding and plaque was from 85.6% to 25.9% one month after the treatment. The results were statistically significant in favour of the laser group (p < 0.05). Microbiological analysis revealed that the pathogens from the red complex decreased 3 times in the control and 6 times in the test group. Therefore, the Er:YAG laser demonstrate pronounced early effectiveness in chronic periodontitis treatment and would be appropriate alternative of the conventional periodontal therapy.