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Obesity is associated with hypothalamic inflammation (HI) in animal models. In the present study we examined the mediobasal hypothalamus (MBH) of 57 obese human subjects and 54 age- and sex- matched non-obese controls by MRI and analyzed the T2-hyperintensity as a measure of HI. Obese subjects exhibited T2-hyperintensity in the left but not the right MBH which was strongly associated with systemic low-grade inflammation. MRI-spectroscopy revealed the number of neurons in the left hypothalamic region to be similar in obese versus control subjects suggesting functional but not structural impairment due to the inflammatory process. To gain mechanistic insights we performed nutritional analysis and 16S rDNA microbiome sequencing which showed that high-fat diet induces reduction of Parasutterella sp. in the gut, which is significantly correlated to MBH-T2-hyperintensity. In addition to these environmental factors we found subjects carrying common polymorphisms in the JNK or the MC4R gene to be more susceptible to HI. Finally, in a subgroup analysis bariatric surgery had no effect on MBH-T2-hyperintensity despite inducing significant weight loss and improvement of peripheral insulin sensitivity. In conclusion, obesity in humans is associated with HI and disturbances in the gut-brain axis which are influenced by both environmental and genetic factors.