Objective: Obesity without metabolic disorder [Ob(+)MD(−)] is a unique subcategory of obesity where individuals are protected from the obesity-related complications. Although conflicting clinical outcomes have been reported, there has been no study of the effects of Ob(+)MD(−) on cerebrovascular disease. In this study, we evaluated the association between the Ob(+)MD(−) phenotype and silent brain infarcts (SBI) in a neurologically healthy population. Subjects/methods: We evaluated a consecutive series of healthy volunteers recruited between January 2006 and December 2013. MD(−) status was assessed using five clinical markers: blood pressure, triglycerides, high-density lipoprotein, fasting plasma glucose, and waist circumference. Obesity was defined when body mass index ≥ 25 kg/m2. SBI was defined as asymptomatic, well-defined lesions with a diameter ≥ 3 mm with the same signal characteristics as the cerebrospinal fluid on T1- or T2-weighted images. Results: A total of 3165 subjects were assessed, and 262 (8%) SBI cases were identified. In multivariate analyses, non-obesity with metabolic disorder [Ob(−)MD(+)] (adjusted odds ratio [aOR] = 1.65, 95% confidence interval [CI] = 1.07–2.56, P = 0.025) and obesity with metabolic disorder [Ob(+)MD(+)] (aOR = 1.75, 95% CI = 1.12–2.75, P = 0.014) were closely associated with SBI after adjustment for confounders. Meanwhile, Ob(+)MD(−) did not show any significant association with SBI (aOR = 0.85, 95% CI = 0.20–3.72, P = 0.832). These findings may indicate that metabolic abnormality, irrespective of obesity status, is a main risk factor of SBI. When we compared SBI burdens between the four metabolic phenotypes, the Ob(+)MD(+) and Ob(−)MD(+) groups had higher rates of multiple lesions than the Ob(+)MD(−) and non-obesity without metabolic disorder groups. Conclusions: The presence of metabolic abnormality, and not obesity per se, is independently associated with the prevalence of SBI in a healthy population.