Investigation of the mechanisms promoting the development of irritable bowel syndrome (IBS) in obese patients is one of the most important issues of modern medicine. We examined 97 patients suffering from IBS. The group of comparison included 10 individuals with obesity. The control group included 21 practically healthy individuals. The levels of C-reactive protein (CRP) in the blood serum, tumor necrosis factor-α (TFNα), transforming growth factor-β1 (TGFβ1), interleukin-10 (IL-10), 8-isoprostane (IP), ceruloplasmin (CP) were examined. Endotoxicosis intensity was identified by the content of average molecular peptides in the blood and the Limulus Amebocyte Lysate (LAL) test. In the case of IBS with prevailing diarrhea, especially its comorbid course with obesity, cytokine imbalance was observed, which was manifested by a decreased amount of IL-10 in the blood serum and increased levels of TNFα and TGFβ1. Patients suffering from irritable bowel syndrome with prevailing diarrhea associated with obesity were characterized by high levels of C-reactive protein, fibrinogen and average molecules, increased content of pro-inflammatory cytokines (TFNα and TGFβ1) with a decreased content of IL-10, as well as imbalance of the pro-oxidant and anti-oxidant blood systems (increased content of 8-isoprostane and ceruloplasmin).