Background: Periodontal disease, the primary cause of tooth loss, is a critical public health concern with a considerable impact on quality of life. It is of interest to explore gender differences in the course of inflammatory periodontal diseases, as well as the prospects of their personalized treatment and prevention in males and females. Aim: To assess the dental health and quantitative composition of periodontal pocket microflora in periodontitis patients, taking into account gender differences. Materials and Methods: The study included 39 patients with moderate chronic generalized periodontitis aged 40–60 years. The diagnosis was made using both primary and secondary dental diagnostic tools. The study had two groups: males (41%, n=16) and females (59%, n=23). The following parameters were assessed: oral hygiene index (OHI-S), severity of gingival inflammation (PMA), and quantitative composition of periodontal pocket microflora (DENTOSCREEN, “Lytech” Co. Ltd., Russia), taking into account gender differences. The study findings were statistically processed using Microsoft Office Excel 2016 with Data Analysis and AtteStat 12.0.5 add-ins. The Shapiro–Wilk test was used. The data are presented as median and interquartile range: Me [Q1; Q3]. The frequency of microorganisms is presented as percentage of the mean and standard error of the mean. The confidence interval was calculated using the Wald method, according to the formula for proportions and frequencies. For small values, the Wald method with Agresti–Coull correction was used. Samples were compared using the following tests: the Mann–Whitney U test was used for quantitative data and Fisher’s angular transformation (φ*emp) for frequency (nominal) attributes. Significant differences were defined as a probability 95% (p 0.05). Results: The quantitative composition of periodontal pocket microflora in patients with moderate periodontitis revealed significant gender differences, as demonstrated by an increase in the count of Fusobacterium nucleatum and Prevotella intermedia, as well as the frequency of Porphyromonas gingivalis, in males compared to females (φ*emp=1.736; p 0.05). Dental health indices confirmed the hypothesis of significant differences between males and females in terms of plaque index (OHI-S) and РМА. In males, poor oral hygiene was reported in 93.7% cases, which was significantly higher (φ*emp=2.04; p 0.05) than in females (69.6%). Moderate gingival inflammation was more prevalent in males, while mild gingival inflammation was more prevalent in females (p 0.05). Conclusion: The study findings emphasize the importance of oral hygiene in the prevention of chronic periodontitis and can be used to improve complex treatment algorithms for patients with periodontal diseases. This includes more frequent dental check-ups and professional oral care sessions, as well as oral hygiene training and monitoring, in males compared to females. Diagnosis by polymerase chain reaction allows for the identification and quantitative determination of DNA from periodontopathogenic bacteria at low concentrations, as well as the justification of treatment algorithms and prediction of treatment outcomes.