Microalbuminuria (MA) is known as a marker for generalized vascular dysfunction. It occurs most commonly in the setting of diabetes and hypertension; however, its association with cerebral small vessel disease (SVD) in community-based elderly remains to be clarified. In this cross-sectional analysis, we evaluated the association between MA and cerebral SVD in total 651 community-based elderly subjects. We assessed cardiovascular risk factors by interviews and physical examinations, including an evaluation of urinary albumin creatinine ratio (UACR). All subjects underwent brain magnetic resonance imaging (MRI) and carotid ultrasonography. As endothelial markers, the serum levels of thrombomodulin (TM) and a tissue-type plasminogen activator/ plasminogen activator inhibitor-1 complex were also studied. The mean TM and UACR were higher in subjects with lacunar infarcts or with moderate white matter hyperintensities (mWMH) on MRI than in those without them. Additionally, the prevalence of lacunar infarcts or mWMH was higher in the highest tertile of UACR level than in the lowest or middle tertile. Furthermore, in logistic regression analysis, the elevation of logarithmically transformed UACR (log UACR) was associated with the higher likelihood for total lacunar infarcts (odds ratio [OR], 1.85 per one log UACR increase), multiple lacunar infarcts (OR, 1.89 per one log UACR increase), and mWMH (OR, 2.15 per one log UACR increase). The present study revealed that levels of urinary albumin are associated with cerebral SVD, independently of traditional cerebrovascular risk factors, in community-based elderly.