Our results show that although genetic variants can be detected with ischaemic stroke, all associations we were able to confirm were specific to a stroke subtype. This finding has two implications. First, to maximise success of genetic studies in ischaemic stroke, detailed stroke subtyping is needed. Second, it implies that different pathophysiological mechanisms are associated with different stroke subtypes and, therefore, drug treatments might have different effects in different stroke subtypes. Most trials of secondary prevention in stroke have included all strokes, with limited stroke subtyping, and further studies with the detailed subtyping would be required to show different pharmacological profiles.