Mortality of obese patients with severe sepsis is higher than non-obese patients. Thus far, a pathophysiologic mechanism has not been identified that explains this higher mortality. The central nervous system is now becoming increasingly recognized as a target organ in sepsis and the systemic inflammatory response syndrome and may hold clues to the deleterious affects of obesity in patients with sepsis syndrome. In this study, obese and non-obese mice were given LPS IP and the brains were harvested 2 hours after injection. The brains were processed and mRNA isolated and hybridized to a microarray chip and processed. Analysis of gene expression demonstrated distinct expression difference between the lean and obese animals. Ontology data supports clear differences between the lean and obese groups in the coagulation system, neuro-endocrine system, lipid transport and insulin receptors. Approximately eighty genes were identified to show 10-fold differential expression between the obese and lean mice.