The field of nutrigenomics recognizes gene-diet interactions, with regard to both the impact of genetic variation on nutrient requirements, and conversely nutrient regulation of the expression of genes. Crohn's disease and ulcerative colitis are inflammatory bowel diseases for which twin studies reveal genetic susceptibility that is impacted by diet and environment. Apparently contradictory data on the role of diet in inflammatory bowel disease would be entirely explainable if genetic variability determined dietary requirements and intolerances. Considering Crohn's disease, we recognize three major classes of genes. The first of these involves bacterial recognition through pattern recognition receptors and autophagy genes, while the second act through secondary immune response, and the third concern epithelial barrier integrity. Despite genetic overlap with CD, the first two groups of genes appear to be less important in ulcerative colitis, while other genes, particularly those involved in barrier function, gain prominence. Case-control studies suggest that these different genetic groups reflect distinct dietary requirements. Such studies suggest nutrigenomic approaches to maintaining disease remission at present, and preventing disease development in the future.