To assess whether high cerebral microbleeds (CMBs) are associated with carotid intima-media thickness (CIMT), a marker of systemic atherosclerosis, we cross-sectionally evaluated participants from a community-based study, the I-Lan Longitudinal Aging Study. The participants' demographics and cardiovascular risk factors were determined by questionnaire and/or laboratory measurements. CIMT was measured by ultrasonography. CMBs were assessed by susceptibility-weighted-imaging on 3 T MRI. Of the 962 subjects [62.5(8.6) years, 44.2% men] included, CMBs were found in 134(14.0%) subjects. Among the subjects with identified CMB's, 85(63.4%) had deep or infratentorial (DI) and 49(36.6%) had strictly lobar(SL) CMBs. After the results were adjusted for age and sex, the analysis revealed that hypertension, hyperlipidemia, obesity, and higher triglyceride levels correlated with DI but not SL CMBs. The subjects with DI CMBs also had a higher mean CIMT and higher prevalence of top quartile CIMT. The multivariate analysis demonstrated that high CIMT (top quartile) significantly predicted the presence of DI CMBs (odds ratio = 2.1; 95% confidence interval = 1.3-3.4; P = 0.004), independent of age, sex, cardiovascular risk factors, and other cerebral small vessel diseases, lacune, and white matter hyperintensity. There was no association between CIMT and SL CMBs. Our results support that there are distinct pathogenesis in DI and SL CMBs.