This document discusses the interaction between nutrients and genes in Celiac Disease from a nutrigenomic perspective. It describes how Celiac Disease has transitioned from a rare childhood disorder to a common autoimmune disease triggered by gluten in genetically susceptible individuals. It discusses how omics sciences can help elucidate relationships between bioactive molecules like gluten, genetic polymorphisms, and the human gut and immune system. Specifically, it focuses on how recent proteomic developments have furthered understanding of gluten toxicity and the roles of genes and the microbiome in disease risk.