Purpose To describe variations in the shape, orientation, and length of the branches of multi-branched thoracoabdominal stent grafts. Method The branches were constructed in situ by attaching a covered stent (Fluency Plus Tracheobronchial Stent Graft; Bard Peripheral Vascular, Tempe, Ariz) to each of four caudally-oriented cuffs on custom-made stent grafts. Pre- and postoperative computed tomography (CT) scans of 38 consecutively treated patients were analyzed using a three-dimensional work station to give the orientation of celiac, superior mesenteric, and right renal and left renal orifices relative to the centerline of the aorta (planned cuff orientation [PCO]) and relative to the centerline of the stent graft (actual vessel orientation [AVO]). The orientation of each cuff (actual cuff orientation [ACO]) was also measured relative to the centerline of the stent graft. These values were used to assess the degree of stent graft malorientation (ACO-PCO), or cuff-to-artery misalignment (ACO-AVO), and combined with measurements of branch length to calculate the resulting lateral displacement (arc distance [AD]) between each cuff and its corresponding arterial orifice and the angle (longitudinal branch angulation [LBA]) between the long axis of the branch and the long axis of the aorta, all in the plane of the aortic surface. Results All 136 branches were inserted as intended. None has since migrated, disconnected, or kinked. In most cases, stent graft orientation was accurate, with a mean ACO-PCO of 18.4 + 12.1 degrees. Cuff-to-artery misalignment was correspondingly low, with a mean ACO-AVO of 19.8 + 14.0 degrees. More than 30 degrees of misalignment was present in 23.2% of branches, yet only 9% (n = 12) had an LBA of >30 degrees. Conclusion Moderate degrees of cuff-to-artery misalignment had no effect on the feasibility of multi-branched stent graft insertion.