From the original anatomic classification of Crohn's disease in 1975, there have been three subsequent published classifications. The most recent, the Vienna Classification arose from a 1998 World Congress of Gastroenterology Working Party that attempted to prospectively design a simple and objective Crohn's disease phenotypic classification that encompassed components of age at onset, anatomic location and disease behavior. Subsequent application of the Vienna Classification to clinical practice has demonstrated that the Crohn's disease phenotype changes markedly over time, with nearly 80% of inflammatory disease ultimately evolving into a stricturing or penetrating pattern of behavior, and 15% undergoing a change in anatomic location. Furthermore, in controlled studies, the ability of inflammatory bowel disease experts to similarly identify the disease phenotypes, using the Vienna classification, ranges from poor to fair. Taken together, these failings markedly limit the utilization of the Vienna classification of Crohn's disease in clinical trails or disease management. Recent advances in determining the genetic linkages associated with Crohn's disease will undoubtedly lead to a revised Crohn's disease classification that will combine genotype with phenotype. Nevertheless, before this new classification can become a reality we will need to reconcile a number of key elements, including; (1) localization and grouping of all inflammatory bowel disease(IBD) gene mutations, (2) discovering the function of the IBD genes, (3) understanding the impact of the environment on phenotypic expression, and, (4) linking to well-defined phenotypic databases that will permit accurate prediction of disease natural history and therapeutic response. Indeed, the consistency of the phenotypic data available may be the greatest single challenge in unraveling the complexities of inflammatory bowel disease and developing a new classification of Crohn's disease.