Abstract Background: This study sought to investigate a possible correlation between the intestinal microbiota, Bacteroidetes and Firmicutes, and obesity in Kazakh school children, aged 7–13 (n = 175). Results: Obese subjects had significantly greater systolic blood pressure, waist and hip circumference, as well as HOMA-IR as compared to normal and overweight participants. In addition, Bacteroides copy number and Bact/Firm ratios were significantly lower in the obese group as compared to the normal and overweight groups (P < 0.0167). This difference is only significant in girls, but not in boys when stratified by gender. Furthermore, a negative correlation between BMI and Bacteroidetes copy number (r = −0.18, P = 0.017) as well as Bact/Firm (r = −0.22, P = 0.003) was observed. Conclusion: An association between reduced gut Bacteroidetes and Bact/Firm ratio with obesity in female Kazakh children was identified. Further studies are necessary to elucidate the mechanism behind these changes as well as the value of determining their presence for predicting obesity.