Genetic factors have been implicated in stroke risk but few replicated associations have been reported. We conducted a genome-wide association study (GWAS) in ischemic stroke and its subtypes in 3,548 cases and 5,972 controls, all of European ancestry. Replication of potential signals was performed in 5,859 cases and 6,281 controls. We replicated reported associations between variants close to PITX2 and ZFHX3 with cardioembolic stroke, and a 9p21 locus with large vessel stroke. We identified a novel association for a SNP within the histone deacetylase 9 ( HDAC9 ) gene on chromosome 7p21.1 which was associated with large vessel stroke including additional replication in a further 735 cases and 28583 controls (rs11984041, combined P = 1.87×10 −11 , OR=1.42 (95% CI) 1.28-1.57). All four loci exhibit evidence for heterogeneity of effect across the stroke subtypes, with some, and possibly all, affecting risk for only one subtype. This suggests differing genetic architectures for different stroke subtypes ; PUBLISHED ; The principal funding for this study was provided by the Wellcome Trust, as part of the Wellcome Trust Case Control Consortium 2 project (085475/B/08/Z and 085475/Z/08/Z and WT084724MA). For details of other funding support see Supplementary MaterialWe thank S. Bertrand, J. Bryant, S.L. Clark, J.S. Conquer, T. Dibling, J.C. Eldred, S. Gamble, C. Hind, M.L. Perez, C.R. Stribling, S. Taylor and A. Wilk of the Wellcome Trust Sanger Institute’s Sample and Genotyping Facilities for technical assistance. We acknowledge use of the British 1958 Birth Cohort DNA collection, funded by the Medical Research Council grant G0000934 and the Wellcome Trust grant 068545/Z/02, and of the UK National Blood Service controls funded by the Wellcome Trust. We thank W. Bodmer and B. Winney for use of the People of the British Isles DNA collection, which was funded by the Wellcome Trust. We thank the following who contributed to collection, phenotyping, sample processing and data management for the different cohorts. Oxford Vascular Study: Annette Burgess, Anila Syed, Nicola Paul. Edinburgh Stroke Study: Martin Dennis, Peter Sandercock, Charles Warlow, Simon Hart, Sarah Keir, Joanna Wardlaw, Andrew Farrall, Gillian Potter, Aidan Hutchison, Mike McDowall. Aberdeen: Alireza Pasdar, Helen Clinkscale. Glasgow: Peter Higgins. ISGS: T. G. Brott, R. D. Brown, S. Silliman, M. Frankel, D. Case, S. Rich, J. Hardy, A Singleton. GEOS: Mary J Sparks, Kathy Ryan, John Cole, Marcella Wozniak, Barney Stern, Robert Wityk, Constance Johnson, David Buchholz. Australian Stroke Genetics Collaborative membership: Jane Maguire, Simon Koblar, Jonathan Golledge, Jonathan Surm, Graeme Hankey, Jim Jannes, Martin Lewis, Rodney Scott, Lisa Lincz; Pablo Moscato; Ross Baker.