The aim of this study was to identify risk factors for erectile dysfunction (ED) in healthy men. A comprehensive risk factor investigation was carried out in a Japanese community. The subjects were 280 healthy male volunteers with an average age of 56 years (range: 20-83 years) who participated in the Iwaki Health Promotion Project in 2006. They were residents of Iwaki district, Hirosaki City, in northern Japan. The participants completed the five-item version of the International Index of Erectile Function (IIEF-5) and the International Prostate Symptom Score (I-PSS) surveys at the site of examination. We measured blood pressure and brachial-ankle pulse wave velocity (baPWV). We also measured risk factors for metabolic syndrome and sex hormones. We compared these risk factors with the IIEF-5 scores. Ninety-five participants (34%) scored 11 points or fewer on the IIEF-5 survey (severe/moderate ED), 154 (55%) scored 12-21 points (mild ED) and 31 (11%) scored 22 points or more (no ED). The prevalence of ED in the Japanese rural community was 89% (249/280). The severe/moderate ED group had significantly higher total I-PSS scores (p = 0.001), baPWV values (p < 0.001) and systolic blood pressure (p < 0.001) than the mild/no ED group. The same group had significantly lower free testosterone (p < 0.001) and dehydroepiandrosterone sulphate (p < 0.001) than the mild/no ED group. Logistic regression analysis revealed significant differences in baPWV (p = 0.003), total I-PSS (p = 0.015) and free testosterone (p = 0.003). Lower urinary tract symptoms, baPWV and free testosterone are independent risk factors for ED in healthy Japanese men.