Background: Causes and consequences of mesenteric embolization after endovascular aorto-iliac procedures have not been studied adequately. Methods: Consecutive patients with mesenteric embolization after endovascular aorto-iliac intervention between 2011 and 2015 (case-group, n = 9) were investigated and compared with age, gender and procedure-matched random controls (n = 36). Results: Compared to the control group, a higher proportion of patients with mesenteric embolization were current smokers (89% vs. 53%; P = 0.048) and had renal insufficiency at admission (44% vs. 11%; P = 0.019). In patients treated for aorto-iliac occlusive disease, aortic irregularity (shagginess) was more severe (P = 0.015), visceral thrombus volume was larger (P = 0.004) and operation-time was longer (P = 0.009) among the case-group. However, no differences were found between cases with mesenteric embolization caused by endovascular aortic aneurysm repair versus controls. Myoglobin, arterial blood lactate, aspartate aminotransferase, alanine aminotransferase and pancreatic amylase levels were elevated in 100%, 67%, 89%, 89%, 89% and 56% of patients with mesenteric embolization, respectively. Overall in-hospital mortality among cases was 33% (3/9). The in-hospital mortality was 17% (1/6) in patients treated with open abdomen therapy, of whom five were managed with stomas. Conclusion: Smoking cessation, careful patient selection and procedure planning with identification of severe shaggy aortas might prevent mesenteric embolization during aorto-iliac procedures. In suspected cases of mesenteric embolization, elevated myoglobin and arterial blood lactate may be indicative of this complication. Aspartate and alanine aminotranferases, as well as pancreatic amylase, are also relevant tests to assess the extent of organ ischaemia. Damage control with open abdomen therapy and the creation of stomas seem justifiable in order to improve survival in this complex situation.