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To improve the quality and effectiveness of medical care for patients with inflammatory periodontal diseases, it is necessary to search for new approaches in both diagnosis and treatment. The aim of our study is to determine the effect of the diode laser on the pathogenic microflora of periodontal pockets and root canals in patients with endo-periodontal lesions (EPL). We carried out a comparative assessment of the bacterial contents of the root canals and periodontal pockets by polymerase chain reaction (PCR) before and after treatment with a diode laser (Doctor Smile Simpler, wavelength 980 nm) for 54 patients with EPL. The control group consisted of 56 patients who were treated according to the generally accepted method, including professional oral hygiene, endodontic treatment, and curettage of periodontal pockets. Evaluation criteria were a qualitative assessment of the content of periodontopathogens in the root canal and periodontal pocket before and after and treatment. As a result of our study, we found a statistically significant (p