The analysis of the relevant literature testifies to the high efficiency of using various mineral waters as a component of integrated treatment of periodontal diseases. Their use is promising as it significantly reduces the medication load on the body. The aim of this study is to evaluate the efficacy of the preventive and therapeutic complex based on mineral water "Morshinska № 1" in the treatment of generalized periodontitis in patients with gastrointestinal diseases. The samples of species composition of anaerobic microorganisms in periodontal pockets were taken from 98 patients immediately after the treatment completion and in 12 -18 month follow up period. The test group included 52 patients with generalized periodontitis who received the above mentioned complex; the control group consisted of 46 patients with generalized periodontitis I-III stages of severity, who received standard therapy to treat periodontal lesions. Detection of pathogens in the oral cavity was carried out by the method of multimeric polymerase-chain reaction. In the long-term follow up, despite a slight increase in the number of patients in the main group who were found to have anaerobic species of microorganisms in their periodontal pockets, the number of the subjects, who were diagnosed as having Helicobacter pylori and Treponema denticola decreased in 2.8 times; the number of patients with Fusobacterium nucleatum and Prevotella intermedia cut down in 2.5 times; and the number of carriers Bacteroides forsythus, Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans lowered in 1.7 times. Among the patients of the control group, who received standard therapy for generalized periodontitis, the number of the subjects who were diagnosed as having anaerobic species of microorganisms in the gingival pockets, the number of the letter went back to the reference values. Thus, the decrease in the number of patients with generalized periodontitis of the test group, who are carriers of anaerobic species of microorganisms, has demonstrated the effectiveness of the prophylactic and treatment complex based on mineral water "Morshinska №1" for the therapy of inflammatory periodontal tissues.