Glycerol kinase deficiency (GKD) is an X-linked inborn error of metabolism that is at the interface of glucose and fat metabolism. Individuals with GKD are at risk for insulin resistance and diabetes mellitus. The purpose of this study was to define the role of GK in insulin resistance in brown adipose tissue by evaluating the changes in gene expression in the glycerol kinase (Gyk) knock out (ko) mouse. Total RNA was extracted from brown fat from 2 day old Gyk ko and wildtype (wt) male mice. Microarray analysis (Affymetrix Mouse Genome 430 2.0 Array, n=4 for each group) determined that there were 495 genes that were differentially expressed (1.5 fold) between ko and wt mice. EASE analysis defined 736 groups with increased and 754 groups with decreased expression in Gyk ko mice. These groups included genes in cell proliferation, transcription, cell death/apoptosis, development, cell differentiation, regulation of cell proliferation, oxidoreductase activity, metabolism, fatty acid, lipid metabolism, carbohydrate metabolism, insulin, and glucose metabolism. Pathway Assist (Stratagene) analyses confirmed direct and/or indirect connectivity of GK and the genes involved in metabolism, glucose, carbohydrate metabolism, insulin, fatty acid, and lipid metabolism that were differentially expressed in the microarray analysis. This confirms that GK deletion is integral to other metabolic networks including carbohydrate and lipid metabolism. In conclusion, GKD in a Gyk ko mouse leads to changes in gene expression in many categories including carbohydrate, glucose, insulin and lipid metabolism. Further evaluation of these genes will allow us to understand the role of GK in insulin resistance and diabetes mellitus.