Objective: Alterations of the oral microbiome have been associated with obesity, possibly based on inflammatory processes mediated by bacteria. Specific bacterial strains have been associated with obesity and periodontal disease. Little is known about the oral microbiome in children. Understanding the relationship between oral health and childhood growth could help identify preventable factors contributing to obesity and related conditions, including onset of menarche which is associated with obesity. Methods: In this pilot study, we investigated the saliva microbiome among 25 girls 7–15 years old (mean 11.1) and their mothers in an inner city dental clinic in New York City. The main outcome measures were body size, presence or absence of menarche and dental practices. We examined associations of microbiome richness, diversity, and relative abundance with pubertal and demographic factors and oral health. Results: Girls had good dental health and a typical rich oral microbiome, based on the Shannon Index of all species detected. Older girls flossed more often and younger girls had more frequent dental check–ups. Microbiome richness among girls was similar to their mothers’, but diversity was greater among mothers than girls. Richness was reduced among mothers with gum bleeding, flossing and increased teeth brushing. Overweight girls had greater diversity and less richness than normal weight girls. Certain bacterial species differed in abundance with respect to whether girls had reached menarche (Flavobacteria, Actinobacteria), overweight (Megasphaera, Lactorbacillales, Lactobacillus) and gingivitis in the girls (Scardovia, Bifidobacteriales, Gemellaceae). Conclusions: Differences found in specific bacteria in the oral microbiome were related to body size and menarche. With increasing interest on studying microbiome variability related to the multifactorial etiology of obesity in children, saliva is capable of providing clinically informative markers of this and related conditions.