Dyslipidemia results from the hepatic overproduction of apoB-100-containing very-low-density lipoprotein (VLDL) and apoB-48-containing chylomicrons from enterocytes. Here, a fructose-fed hamster model of insulin resistance is used to develop a proteomic profile of protein factors in the secretory pathway that are altered in response to the onset of insulin resistance. Lipoproteins are assembled in the ER and Golgi apparatus of hepatocytes and enterocytes. We have profiled ER- and Golgi-associated proteins from insulin resistant and control hepatocytes and enterocytes, with the intention of identifying proteins involved in insulin signaling attenuation and lipoprotein overproduction. Differentially expressed in the hepatic secretory pathway with fructose-feeding, were cellular chaperones and proteins involved in oxidative stress. In the enteric ER, fructose-feeding caused the differential expression of proteins involved in glucose metabolism. These findings have increased our understanding cellular responses accompanying the onset of insulin resistance and metabolic dyslipidemia.