Purpose: To compare the impact of 2 commercially available custom-made fenestrated endografts on patient anatomy. Materials and Methods: The records of 234 patients who underwent fenestrated endovascular aneurysm repair for abdominal aortic aneurysm from March 2002 to July 2016 in 2 hospitals were screened to identify those who had pre- and postoperative computed tomography angiography assessments with a slice thickness of ≤2 mm. The search identified 145 patients for further analysis: 110 patients (mean age 72.4±7.1 years; 94 men) who had been treated with the Zenith Fenestrated (ZF) endograft and 35 patients (mean age 72.3±7.3 years; 30 men) treated with the Fenestrated Anaconda (FA) endograft. Measurements included aortic diameters at the level of the superior mesenteric artery (SMA) and renal arteries, target vessel angles, target vessel clock positions, and the target vessel tortuosity index. Variables were tested for inter- and intraobserver agreement. Results: There was a good agreement between observers in all tested variables. The native anatomy changed in both groups after endograft implantation. In the ZF group, changes were seen in the angles of the celiac artery (p=0.012), SMA (p=0.022), left renal artery (LRA) (p<0.001), and the right renal artery (RRA) (p<0.001); the aortic diameter at the SMA level (p<0.001); and the LRA (p<0.001) and RRA (p<0.001) clock positions. In the FA group, changes were seen in the angles of the LRA (p=0.001) and RRA (p<0.001) and in the SMA tortuosity index (p=0.044). Between group differences in changes were seen for the aortic diameters at the SMA and renal artery levels (p<0.001 for both) and the LRA clock position (p=0.019). Conclusion: Both custom-made fenestrated endografts altered vascular anatomy. The data suggest a higher conformability of the Fenestrated Anaconda endograft compared with the Zenith Fenestrated.