Obesity is a growing problem all over the world and results from chronic imbalance of energy intake and energy expenditure. The etiology of obesity is very complex. It is estimated that the genetic differences among individuals cause 40 - 70% of the difference in susceptibility to develop obesity. The gene FTO (eng. Fat mass and obesity-associated) is a gene with the largest effect on body mass index and the risk of developing obesity. The aim of this study is to determine the differences in the distribution of each genotype polymorphism rs9939609 (AA, AT or TT) and differences in oral microbiome between obese and normal weight individuals. Many studies on various populations confirmed association of the polymorphism rs9939609 in the first intron of the FTO gene with an increased susceptibility of obesity development and type 2 diabetes, and with this study by real-time PCR frequency of this polymorphism in women Zagreb County was determined. The difference in the microbiome was revealed by identification of the microorganisms from saliva of the two tested groups. Participants completed a questionnaire that gave insight into their lifestyle, diet and diseases and these data supplemented the results of genotyping and identification of bacteria of the oral cavity. The results of this study should contribute to a better understanding of the role of FTO gene polymorphism rs9939609, oral microbiome and lifestyle in the development of obesity in this area.