A meta-analysis of 15 genome-wide association studies of inflammatory bowel disease (IBD) has been carried out and analysed along with data from an Immunochip study. One hundred and sixty-three loci were identified — the most for any complex disease to date. Many IBD loci were implicated in other immune-related disorders, and there was an overlap between IBD and mycobacterial infection susceptibility loci. Evidence for directional and balancing selection at IBD loci was also uncovered.