Magnetic resonance imaging allows detailed visualization of the thoracic aorta and is not limited by air artefacts or insonation angles like transoesophageal echocardiography (TEE). Thus the aortic arch can be investigated with higher accuracy, and additional embolic high-risk sources such as complex plaques can be additionally detected by MRI in patients with cryptogenic stroke. Furthermore, MRI provides exact 3D plaque localisation and can be combined with multidirectional 3D MRI velocity mapping. In this way, previously not demonstrable retrograde flow paths originating at complex descending aortic plaques reaching the supra-aortic great arteries can be identified as the probable stroke mechanism in certain patients. The same technique can also be applied to the carotid arteries. This allows analysing the complex 3D helical flow within the internal carotid artery as well as measuring absolute flow velocities and wall shear stress in combination with data on vessel anatomy derived from conventional MR angiography. It is the purpose of this work to describe the state of the art of these modern MR imaging techniques and their potential to identify potential stroke mechanisms, and to analyse the particular role of individual haemodynamic factors on the development of local atherosclerosis.