Obesity is associated with hypertension. However, it is controversial which obesity index, body mass index (BMI) or waist circumference (WC), is more strongly associated with hypertension. We compared the cross-sectional associations of BMI and WC with hypertension. Logistic regressions using hypertension as a dependent variable and age, BMI, WC, fasting plasma glucose, triglycerides, high-density lipoprotein cholesterol, smoking status, drinking status, and physical activity as independent variables were performed using data from apparently healthy 1,803 Japanese men aged 49.9 ± 9.0 and 1,150 women aged 49.5 ± 9.0 excluding subjects with a history of cardiovascular disease, or with antidiabetic, antihypertensive and/or antihyperlipidemic medications. The odds ratio [95% confidence interval] of 1 kg/m2 increase in BMI and that of 1 cm increase in WC for diagnosing hypertension were 1.23 [1.11–1.36] (p < 0.0001) and 0.99 [0.95–1.02] (p = 0.4) in men and 1.35 [1.16–1.58] (p < 0.0001) and 0.97 [0.91–1.03] (p = 0.4) in women, respectively. Thus, BMI, but not WC, was independently associated with hypertension in apparently healthy Japanese men and women.