OBJECTIVE: To compare 30 day outcomes and costs of fenestrated and branched stent grafts (f/b EVAR) and open surgery (OSR) for the treatment of complex abdominal aortic aneurysms (AAA) and thoraco-abdominal aortic aneurysms (TAAA). METHODS: The multicenter prospective registry WINDOW was set up to evaluate f/b EVAR in high risk patients with para/juxtarenal AAA, and infradiaphragmatic and supradiaphragmatic TAAA. A control group of patients treated by OSR was extracted from the national hospital discharge database. The primary endpoint was 30 day mortality. Secondary endpoints included severe complications, length of stay, and costs. Mortality was assessed by survival analysis and uni/multivariate Cox regression analyses using pre- and post-operative characteristics. Bootstrap methods were used to estimate the cost-effectiveness of f/b EVAR versus OSR. RESULTS: Two hundred and sixty eight cases and 1,678 controls were included. There was no difference in 30 day mortality (6.7% vs. 5.4%, p = 0.40), but costs were higher with f/b EVAR (euro38,212 vs. euro16,497, p < .001). After group stratification, mortality was similar with both treatments for para/juxtarenal AAA (4.3% vs. 5.8%, p = .26) and supradiaphragmatic TAAA (11.9% vs. 19.7%, p = .70), and higher with f/b EVAR for infradiaphragmatic TAAA (11.9% vs. 4.0%, p = .010). Costs were higher with f/b EVAR for para/juxtarenal AAA (euro34,425 vs. euro14,907, p < .0001) and infradiaphragmatic TAAA (euro37,927 vs. euro17,530, p < .0001), but not different for supradiaphragmatic TAAA (euro54,710 vs. euro44,163, p = .18). CONCLUSION: f/b EVAR does not appear justified for patients with para/juxtarenal AAA and infradiaphragmatic TAAA fit for OSR but may be an attractive option for patients with para/juxtarenal AAA not eligible for surgery and patients with supradiaphragmatic TAAA. CLINICAL TRIAL REGISTRATION: http://www.clinicaltrials.gov/ct2/show/NCT01168037; identifier: NCT01168037 (WINDOW registry).