Ischemic stroke in younger people is common, and often remains unexplained. There is a well-documented association between unexplained stroke in younger people, and the presence of a patent foramen ovale. Therefore, in the absence of a clear cause of stroke, the heart is often assessed in detail for such lower risk causes of stroke. This usually involves imaging with a transesophageal echo, and investigation for a right-to-left shunt. An understanding of the anatomy of the atrial septum, and its associated abnormalities, is important for the stroke neurologist charged with decision making regarding appropriate secondary prevention. In this paper, we review the development and anatomy of the right heart with a focus on patent foramen ovale, and other associated abnormalities. We discuss how the heart can be imaged in the case of unexplained stroke, and provide examples. Finally, we suggest a method of investigation, in light of the recent European Association of Echocardiography guidance. Our aim is to provide the neurologist with an understanding on how the heart can be investigated in unexplained stroke, and the significance of abnormalities detected.