Although metabolic syndrome (MS) is likely to be associated with nonalcoholic fatty liver disease (NAFLD), visceral fat type MS and subcutaneous fat type MS have not been distinguished. In this study, we divided persons with MS into those with visceral and subcutaneous fat types by ultrasonography (US), and elucidated differences between these types of MS in Japanese males. The subjects were 628 males with MS who underwent a medical checkup including abdominal US. We examined for the presence of fatty liver and investigated biochemical parameters, and we also made a distinction between visceral and subcutaneous fat types of MS by US. Total cholesterol (T-CHO), low-density lipoprotein cholesterol (LDL-C), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and the frequency of fatty liver were significantly higher in visceral fat type MS than in subcutaneous fat type MS. On logistic regression analysis with NAFLD (in our study, fatty liver with ALT ≥31 IU/l was defined as NAFLD) as a dependent variable, the age, body mass index (BMI), AST, and visceral fat type MS were significant risk factors for NAFLD. BMI, AST, and visceral fat type MS were predictors of an increased prevalence of NAFLD [odds ratios (ORs) = 1.903, 12.06, and 2.617; 95% confidence intervals (CIs) = 1.122-3.228, 7.053-20.61, and 1.741-3.935; p = 0.017, <0.001, and <0.001, respectively). Japanese males with visceral fat type MS are more likely to have dyslipidemia, fatty liver, and liver dysfunction than those with subcutaneous fat type MS. Visceral fat type MS is one of the most significant risk factors for NAFLD in Japanese males with MS.