We believe the future clinical application of genomic information in IBD will lie in the use of a combination of “gene-chips” designed specifically for variation relevant to IBD and ultimately in the cataloging of an individual’s entire collection of genomic variation through whole-genome sequencing. In the short term, the expansion of pharmacogenomic tests and biomarker assessments are likely to have the most significant influence on prescribed IBD treatment therapies and disease management. Moreover, these pharmacogenomic and biomarker data are likely to benefit greatly from the ongoing genomic analyses, as they can begin to put these data in the proper genetic context as they relate to monitoring and assessing these effects across different ethnic and racial populations. Although mentioned only briefly in this review, a clearer understanding of environmental triggers of IBD will be of utmost importance to furthering our understanding of the genetic factors and the complex interactions that are likely to exist between genes and environment. The successful identification of genetic factors influencing IBD risk has been accelerating over the last few years and is likely to continue. Currently, these genetic factors provide no direct bearing on clinical treatments or therapies. Instead, these findings aid in our understanding of disease pathogenesis and indirectly to potential for development of novel therapeutics. In the near term, they may be able to provide some additional utility in distinguishing CD cases from UC cases. Future use of genomic information and its role in diagnosing and managing IBD patients is promising but not yet mature. The search for the so-called missing heritability in IBD will undoubtedly continue to uncover novel genes, biological pathways, and the likely interplay between genetic variation and environmental factors. The creation of a customized gene-chip (allowing for the creation of a patient-specific cataloging of IBD relevant genetic information), for use in clinical practice, is an almost certainty. Although this information will likely provide significant aid to diagnostics and treatment, it is doubtful that it could ever fully stand alone. It must be accompanied by thorough clinical evaluation and data, a more complete characterization of a patient’s potential environmental triggers, and integration with other known pharmacogenomic and molecular biomarker information.