Stent graft devices for the treatment of abdominal aortic aneurysms (AAAs) are being increasingly used worldwide. Yet, during modelling and optimization of these devices, as well as in clinical practice, vascular sections are idealized, possibly compromising the effectiveness of the intervention. In this study, we challenge the commonly used approximation of the circular cross-section of the aorta and identify the implications of this approximation to the mechanical assessment of stent grafts. Using computed tomography angiography (CTA) data from 258 AAA patients, the lumen of the aneurysmal neck was analysed. The cross-section of the aortic neck was found to be an independent variable, uncorrelated to other geometrical aspects of the region, and its shape was non-circular reaching elliptical ratios as low as 0.77. These results were used to design a finite element analysis (FEA) study for the assessment of a ring stent bundle deployed under a variety of aortic cross-sections. Results showed that the most common clinical approximations of the vascular cross-section can be a source of significant error when calculating the maximum stent strains (underestimated by up to 69%) and radial forces (overestimated by up to 13%). Nevertheless, a less frequently used average approximation was shown to yield satisfactory results (5% and 2% of divergence respectively).