Cerebral small vessel diseases (CSVD), such as white matter hyperintensities (WMH), have been acknowledged as a cause of brain atrophy. However, the relationship between brain volumes and cerebral microbleeds (CMBs) has not yet been determined. We aimed to evaluate whether the presence and topography of CMBs are associated with altered volumes of gray matter (GMV) and white matter (WMV). Non-stroke and non-demented subjects were prospectively recruited from the I-Lan Longitudinal Aging Study. High-resolution 3-T MRI was performed to quantify total and regional WMV and GMV, including Alzheimer’s disease-susceptible areas. CMBs were assessed with susceptibility-weighted imaging. Six hundred and fifty-nine subjects (62.1 ± 8.3 years, 290 (44%) men) were included. Thirty-two (4.9%) subjects had strictly lobar CMBs (SL-CMBs) and 51 (7.7%) had deep or infratentorial CMBs (DI-CMBs). We observed an association between CMBs and WMV, independent of age, sex, and vascular risk factors; the direction of association depended on the location of the CMBs. The SL-CMB group had an increased total, frontal, and occipital WMV compared with the no-CMB group, which remained significant after adjusting for other CSVDs (WMH volumes and lacune numbers). In contrast, the DI-CMB group had a decreased occipital WMV compared to the no-CMB group. However, this significance disappeared after taking other CSVDs into consideration. Our results showed no relationship between CMBs and GMV. In conclusion, the increased WMV in non-stroke, non-demented subjects with SL-CMBs observed here provides insight into the early pathogenesis of SL-CMBs. This may be a result of increased water content or amyloid accumulation.