For most immune-mediated diseases, the main determinant of patient well-being is not the diagnosis itself but instead the course that the disease takes over time (prognosis). Prognosis may vary substantially between patients for reasons that are poorly understood. Familial studies support a genetic contribution to prognosis, but little evidence has been found for a proposed association between prognosis and the burden of susceptibility variants. To better characterize how genetic variation influences disease prognosis, we performed a within-cases genome-wide association study in two cohorts of patients with Crohn's disease. We identified four genome-wide significant loci, none of which showed any association with disease susceptibility. Conversely, the aggregated effect of all 170 disease susceptibility loci was not associated with disease prognosis. Together, these data suggest that the genetic contribution to prognosis in Crohn's disease is largely independent of the contribution to disease susceptibility and point to a biology of prognosis that could provide new therapeutic opportunities. ; This work was supported by the NIHR Cambridge Biomedical Research Centre (in particular John Todd and the NIHR BRC Genomics Theme), Crohn's and Colitis UK (Medical Research Award M/14/2), the Evelyn Trust (17/07), and the Medical Research Council (Programme Grant MR/L019027/1). J.C.L. is supported by a Wellcome Trust Intermediate Clinical Fellowship (105920/Z/14/Z) and D.B. by a Marie Curie PhD Fellowship (TranSVIR FP7-PEOPLE-ITN-2008 #238756). C.A.A. is supported by the Wellcome Trust (098051). K.G.C.S. is an NIHR Senior Investigator. This study makes use of data generated by the UK10K Consortium, derived from samples from ALSPAC and DTR cohorts. A full list of the investigators who contributed to the generation of the data is available from www.UK10K.org. Funding for UK10K was provided by the Wellcome Trust (WT091310).