Background Apart from nondippers’ impact on cardiovascular events, the prevalence of isolated nocturnal hypertension (INH) and its consequences on both the heart and brain were not clearly investigated in the general population. Methods and Results The participants underwent ambulatory blood pressure monitoring evaluations for arterial stiffness, echocardiography, and brain magnetic resonance imaging. They were grouped into normotension, INH, and overt diurnal hypertension, based on ambulatory blood pressure monitoring and history of antihypertensive treatment. White matter hyperintensity, arterial stiffness, and echocardiographic parameters were compared. Of the 1734 participants, there were 475 (27.4%) subjects with normotension, 314 with INH (18.1%), and 945 with overt diurnal hypertension (54.5%). Prevalence of INH was not different between sex or age. Of INH, 71.3% (n=224) was caused by elevated diastolic blood pressure. After multivariable adjustment, INH showed higher pulse wave velocity ( P <0.001) and central systolic blood pressure ( P <0.001), left ventricular mass index ( P =0.026), and worse left ventricular diastolic function (early diastolic mitral annular velocity) ( P <0.001) than normotension. Mean white matter hyperintensity scores of INH were not different from normotension ( P =0.321), but the odds for white matter hyperintensity presence were higher in INH than normotension (odds ratio, 1.504 [95% CI, 1.097–2.062]; P =0.011). Conclusions INH was common in the general population and associated with increased arterial stiffness, left ventricular hypertrophy, and diastolic dysfunction. White matter hyperintensity was more likely to be present in the INH group than in the normotension group. The use of ambulatory blood pressure monitoring should be encouraged to identify masked INH and prevent the occurrence of cardiovascular events.