It is still debated whether non valvular atrial fibrillation (NVAF) may be responsible for "silent" lacunar lesions. The aims of our study were to compare the prevalence of subcortical lacunar infarctions in highly selected elderly subjects with or without NVAF, and to investigate the positive relationship of such lesions to the impairment in cognitive and physical functions. Thirty-eight patients with NVAF (mean age 80.6 years) were compared with 40 patients in sinus rhythm (mean age 80.4 years). Exclusion criteria were previous stroke or transient ischemic attacks, significant lesions of extracranial arteries, and any previous disease leading to cognitive impairment or potentially interfering with cognitive functions. A cranial computed tomogram was performed in every case, and the number of lacunae was recorded. Cognitive status and mood were assessed by means of Mini Mental Status Examination and the Geriatric Depression Scale, respectively. The number of impaired basic and instrumental activities of daily living (BADL e IADL) was also recorded. A significantly higher percentage of patients with lacunar lesions was detected in the NVAF group. The MMS score was lower in these patients, but did not reach significant levels. In univariate analysis, the presence of lacunae was found to be significantly associated with age, systolic blood pressure and atrial fibrillation, but, in a multiple logistic regression model, only age and atrial fibrillation retained a significant association. Similarly, in univariate analysis, a low MMS score was found to be related to age, systolic blood pressure, leukoaraiosis and both the presence and the number of lacunar lesions. In multivariate analysis, only age and the number of lacunae were significantly associated with a low MMS. It is concluded that in elderly patients NVAF is associated with subcortical ischemic lesions which may contribute to the impairment of cognitive function.