Background: The aim was to determine the occurrence, consequences and risk factors for brain white matter hyperintensities (WMH) assessed in magnetic resonance imaging (MRI) in low-risk patients with paroxysmal atrial fibrillation (AF) undergoing radiofrequency pulmonary vein isolation (PVI-RF). Methods: 74 patients with AF (median 58.5 years (IQR 50–63), 45 male) were included. Before and after a minimum of 6 months after PVI-RF, a brain MRI and a mini-mental state examination (MMSE) were performed. Results: Baseline WMH lesions were found in 55 (74.3%) patients and in 48 from 62 (77.4%) patients after PVI-RF. The WMH lesions were more frequent among older patients, with a higher CHA2DS2-Vasc (C—Congestive heart failure/LV dysfunction, H—Hypertension, A—Age, D—Diabetes mellitus, S—Stroke, V—Vascular Disease, Sc—Sex category). Factors affecting the severity of the WMH were: older age, the co-existence of the PFO and coronary artery disease (CAD). After a follow-up period, the factors predisposing to brain WMH lesions occurrence (age, higher BMI and CHA2DS2-Vasc score) and to the more advanced changes (age, higher CHA2DS2-Vasc score, CAD, PFO) were obtained. Conclusions: The presence and severity of cerebral microembolism are associated with age, higher CHA2DS2-Vasc score and the coexistence of PFO and CAD. PVI-RF procedure and its efficacy does not influence on MRI lesions. In this population, cerebral microembolism is not related to cognitive impairment.