The objective of the present study was to elucidate the glycemic and lipid blood plasma profiles in the patients presenting with chronic generalized periodontitis (CGP) and the relationship between the body mass index and the clinical course of CGP. A total of 99 patients allocated to two groups were enrolled in the study. Group 1 was comprised of 20 patients with body mass index (BMI) of < 25 kg/m^2, group 2 consisted of 73 patients having BMI => 25 kg/m^2. Mucosal biopsies from the oral cavity and the intestines (feces) were analyzed by “real time” PCR. The standard therapy of periodontitis was supplemented by the treatment with ubichinon compositum injections (2 ml intramuscularly twice weekly) and Simbiolakt-Compositum probiotic (1 sachet per day) in order to reduce oxidative stress (systemic inflammation) and compensate for dysbiosis of the gastrointestinal tract. The total duration of the treatment was 21 days. It resulted in the reduction of the severity of proinflammatory processes and oxidative stress. The relationship between the growing severity of chronic generalized periodontitis (CGP) and the body mass index (BMI) was documented. It is concluded that the characteristics of carbohydrate and lipid metabolism during the early stages of the development of metabolic syndrome (MS) should be interpreted as the consequence of the general biological reaction to chronic inflammation induced and maintained by the disturbances of dysbiosis of the gastrointestinal tract.