Aggressive enteral nutrition and poor intestinal perfusion are hypothesized to play an important pathogenic role in non-occlusive small bowel necrosis. This study tests the hypothesis that glucose and glutamine transport are differentially regulated during hypoxia regardless of the luminal nutrient present. Sprague-Dawley rats (247±3 g; n=16) were randomized to receive 1 hour of intestinal hypoxia or serve as normoxic controls. During this hour, jejunal loops were randomized to receive in situ perfusions of mannitol, glucose or glutamine. When compared to normoxic groups, glucose but not glutamine transport was impaired (P < 0.001) during hypoxia. Messenger RNA abundance of the sodium glucose co-transporter (SGLT-1) and neutral basic amino acid transporter, B^o, did not differ with hypoxia or nutrient perfused. Jejunal brush-border SGLT-1 abundance was decreased (P = 0.039) with hypoxia, however total cellular SGLT-1 protein abundance did not differ among treatment groups. These data indicate that SGLT-1 activity is regulated during hypoxia at the post-translational level. Additional information regarding the mechanisms regulating nutrient transport in the hypoperfused intestine is critical for optimizing the composition of enteral nutrient formulas.