Background: Aortic arch atheroma (AAA) has been accepted as a possible embolic source in patients with ischemic stroke, especially cryptogenic stroke. However, despite its well-known role as a risk factor for stroke, research focused on the mechanism or characteristics of stroke caused by AAA is insufficient. In this study, we aimed to evaluate clinical and radiological characteristics including lesion pattern on DWI in acute stroke patients associated with vulnerable AAA detected by multidetector row computed tomography (MDCT). Methods: From September 2008 through May 2011, patients who presented with acute ischemic stroke and underwent MDCT were found in a prospective stroke registry. Patients without evident stroke etiology were included and classified by presence of vulnerable AAA. Vulnerable AAA was defined as (i) at least 6 mm thick adjacent to the aortic wall; (ii) ulcerated plaque, or (iii) soft plaque. Soft plaque was defined as the presence of clearly visualized area of hypoattenuation (<80 Hounsfield units) suggestive of thrombus. The patients without vulnerable AAA were classified as no/simple AAA group. The characteristics of diffusion-weighted MRI (DWI) lesions were analyzed in terms of the number and size of the lesions, and the involved vascular territories. Results: A total of 63 cryptogenic stroke patients were included in this study. Vulnerable AAA was observed in 15 (23.8%) patients. The patients with vulnerable AAA were older than those with no/simple AAA (p = 0.026). DWI analysis revealed that the vulnerable AAA group had a greater chance of having multiple and small lesions in multiple vascular territories that were mainly located in cortical and border-zone regions than the no/simple AAA group. Multiple logistic regression analysis showed that age (odds ratio 1.17; 95% confidence interval 1.02–1.34) and multiple small lesions in multiple vascular territories (odds ratio 33.18; 95% confidence interval 4.26–258.45) were independently associated with vulnerable AAA. Conclusion: Vulnerable AAA is independently associated with a DWI pattern characterized by multiple small scattered lesions in multiple vascular territories in conjunction with age. It may help determine stroke mechanism quickly and easily, and provide more information about the pathomechanism of vulnerable AAA-related stroke.