Background: Few studies addressed the prevalence of cerebral microbleeds (CMB) and associated risk factor profile in Egyptian ischemic cerebral stroke patients with atrial fibrillation (AF). Methods: The prevalence of CMB was estimated in 150 cases of AF ischemic stroke patients and compared to the prevalence in 150 age- and sexmatched controls of ischemic stroke patients without AF. CMB-associated risk factors were identified by comparing AF ischemic stroke patients with and without CMB. All participants were subjected to complete general, neurological examination, and magnetic resonance imaging. Results: The prevalence of CMBs in ischemic stroke with and without AF was 40.7% and 49.3%, respectively. Age, hypertension, diabetes mellitus, past history of stroke, antiplatelet, anticoagulant, National Institutes of Health Stroke Scale, CHA2DS2VASc, and white matter lesions (WML) were significant risk factors associated with CMB on univariate analysis. On multivariable logistic regression analysis, age (odds ratio [OR] 1.1, confidence interval [CI] 1.02-1.13), hypertension (OR 3.2, CI 1.19-8.81), anticoagulant (OR 3.3, CI 1.17-9.40), and WML (OR 9.6, CI 3.49-26.3) were the only independent risk factors associated with the presence of CMBs. Conclusions: AF in ischemic stroke patients was not associated with higher prevalence of CMBs. Old age, hypertension, anticoagulant treatment, and WML were the independent risk factors associated with CMB in AF ischemic stroke patients. Our results suggest that elderly hypertensive AF ischemic stroke patients maintained on anticoagulant therapy should be screened for the incidence of CMBs and monitored regularly for the development of intracerebral hemorrhage.