Short chain fatty acids (SCFA) are the main bacterial metabolites of colonic fermentation processes. The physiological relevance of the SCFA for the host outside the gastrointestinal tract is getting increased attention. In this review we will focus on the effect of SCFA on inflammation processes in the host in relation to insulin resistance. Obesity has been associated with a pro-inflammatory state of the adipose tissue that is associated with whole body insulin resistance leading to type 2 diabetes. Recently, two G protein-coupled receptors (GPCR) for SCFA, GPCR 41 and GPCR43, were described that are mainly expressed by immune cells but also by adipose tissue. Propionate can induce the satiety hormone leptin and reduce expression of inflammatory cytokines and chemokines indicating that SCFA have anti-inflammatory effects in human adipose tissue. In addition, in human nutritional experiments we observed that whole grain products could counteract a glucose-induced tumour necrosis factor α and interleukin-6 increase which was associated with increased plasma butyrate concentrations. This suggests that dietary fibre can produce a SCFA profile that could have anti-inflammatory effects in the body. The physiological relevance of these observations especially in relation to obesity-associated inflammation and insulin resistance is discussed.