Endovascular treatments have become increasingly common for patients with a variety of thoracic aortic pathologies. Although considered less invasive than traditional open surgical approaches, they are nonetheless complex procedures. Patients undergo manipulation of an often calcified aorta near the origin of the carotid and subclavian vessels and have stents placed in a curved vessel adjacent to a perpetually beating heart. These stents can obstruct blood flow to the spinal cord, induce an inflammatory response, and in rare cases erode into the adjacent trachea or esophagus. Renal complications range from contrast-induced nephropathy to hypotension and ischemia to dissection. Emboli can lead to strokes and mesenteric ischemia. These patients have complex medical histories, and skilled perioperative management is critical to achieving the best clinical outcomes. Here, we review the medical management of the most common complications in these patients including stroke, spinal cord ischemia, renal injury, retrograde dissections, aortoesophageal and aortobronchial fistulas, postimplantation syndrome, mesenteric ischemia, and endograft failure.