Adipose tissue, being  a source of chronic low-grade inflammation, activates cells of the immune system by producing cytokines and chemokines. The balance between pro- and anti-inflammatory molecules and their relationship with blood bacterial DNA in obese children and adolescents has not been studied sufficiently. This study aimed to find patterns of interaction between fractions of bacterial families in healthy and obese children, analyze cytokine levels and their relationship with blood bacterial DNA content, evaluate alpha diversity of blood microbiome and similarities of blood and fecal microbiomes. We examined 163 individuals (children and adolescents), who were divided into 2 groups, obese (n = 80, obesity classes I through III) and healthy (n = 83). The material sampled and studied was venous blood. Only individuals that have not been taking antibiotics, pro- and prebiotics for at least 3 months before the study were included. The methods employed were multiplex ELISA (enzyme immunoassay) and 16S rRNA gene sequencing (region V3–V4). From the angle of bacterial families, we found differences in their content (fractions) in blood microbiome and the frequency of isolation of their DNA therein. Nineteen  families accounted for over three quarters of all bacterial DNA identified in the blood. In obese children, one of the dominating roles was played by Ruminococcaceae, with their DNA a key part of the microbiome's alpha diversity, while in healthy participants this could be said about Bacteroidaceae. Analyzing beta diversity, we found that in obese children, fecal and blood microbiomes differed significantly, which indicates, mainly, extra-intestinal translocation of bacterial DNA. Obese children exhibited increased content of IL17A (p = 0.017) and PD-L1 (p = 0.021); there were differences in blood microbiome between groups. We identified the patterns of interaction between bacterial DNA fractions, and assessed cytokine levels.