Significant advances have occurred in identifying the types of malnutrition and specific nutrient deficits that adversely affect clinical outcome in patients with inflammatory bowel disease (IBD). Innovative nutritional therapies are being developed to correct these deficits. The traditional clinical practice of prescribing bowel rest for patients with IBD is undergoing rigorous scientific scrutiny. Moreover, it is now hypothesized that in selected patients with IBD, it may be more advantageous to feed into the gut those fuels that are preferentially metabolized by its mucosa rather than to prescribe bowel rest, which starves the gut and produces intestinal atrophy and dysfunction. Examples of these fuels include glutamine, the preferred enterocyte fuel, and butyrate, the major energy source for the colonocyte. Additionally, the ω-3 fatty acids, commonly termed fish oils, provide important immunocompetence to the gut barrier and may benefit patients with IBD. As a result of reduced costs and improved morphologic and functional benefits to the gut, studies in patients with IBD continue to confirm the importance of providing total enteral nutrition rather than total parenteral nutrition.