Clinical evidence supports the occurrence of intermittent diarrhea in many type 1 diabetes mellitus (T1DM) patients. Others and we found that net fluid absorption rate is dramatically lower in the ileum of T1DM murine models. However, the identity of molecules that contribute to fluid malabsorption in the gut remains unknown. Considering the importance of ion transporters and channels for intestinal fluid absorption, we reasoned that their expression level at the luminal membrane is altered under diabetic conditions. To this end, we analyzed the brush border membrane vesicles (BBMVs) from the ileum of control and DM mice by proteomic analysis. The expression levels of Cl-/HCO3- exchanger SLC26A3/DRA and cystic fibrosis transmembrane conductance regulator (CFTR) were not significantly different between control and DM mice. Cl-/HCO3- exchanger Slc26a6/PAT1 and Na+/H+ exchanger 3 (NHE3) were not detected. Interestingly, cytoskeleton scaffold proteins that regulate NHE3, including NHERF1-3 and ezrin, were all significantly lower in diabetic animals.