In contrast to its prevalence in the surrounding vasculature, occurrence of primary atherosclerotic disease in the superior mesenteric artery (SMA) is rare (Glagov et al., 1988. Hemodynamics and atherosclerosis, Insights and perspectives gained from studies of human arteries. Archives of Pathology and Laboratory Medicine 112(10), 1018–1031; Hansen et al., 2004. Mesenteric artery disease in the elderly. Journal of Vascular Surgery 40(1), 45–52). We hypothesise that this sparing might be attributed to more favourable haemodynamic characteristics in the SMA than in other vessels locally. Dynamic magnetic resonance imaging (MRI) images established that the SMA is highly mobile (Jeays, 2006. Investigation of blood flow in the superior mesenteric artery and its potential influence on atheroma and gut ischaemia. Ph.D. Thesis, University of Sheffield), and thus that an analysis based on rigid geometry might be inappropriate. This paper describes an efficient methodology for the construction of a patient-specific, time-dependent model of an arterial segment and reports the results of a haemodynamic characterisation of the SMA for one individual. A transient computational fluid dynamic (CFD) model was constructed by morphing a parametric mesh constructed from simple geometric primitives. This process has the merit that it is easy to control the element size distribution mapped onto the original geometric primitives. It is robust in operation, and is ideally suited to the generation of dynamic CFD meshes of arterial systems that are free from major pathology. Flow boundary conditions were determined based on phase contrast MRI velocity measurements. Comparative studies with rigid walls and with moving walls, based on the transient data, indicated that, despite the significant motion of the SMA (radial dilation of the order of 10% and translation of the order of the radius), the maximum (spatially and temporally-resolved) wall shear stresses changed by no more than 21.6% of a global norm, and the average change was less than 2.1%.