Cardiovascular disease (CVD) remains the leading cause of death, but the risk factors for CVD differ between men and women. Although carotid intima-media thickness (IMT), carotid plaque, and pulse wave velocity (PWV) are useful atherosclerotic parameters, patient backgrounds have differed in previous reports. Therefore, this study aimed to investigate gender differences in associations between these three parameters and traditional risk factors in the same population. We enrolled 3888 participants (women: 743) who underwent routine health checkups. High IMT, high carotid plaque score (PS), or high brachial–ankle PWV (baPWV) were defined by the median values for each gender. We analyzed the association between each parameter and atherosclerotic risk factors, such as obesity, smoking, blood pressure (BP) elevation, impaired fasting glucose (IFG), and dyslipidemia (DL). In both sexes, BP elevation was the only common risk factor for high IMT, high PS, and high baPWV in the multivariate logistic regression analysis adjusted for age. In men, IFG and DL were common risk factors for the three parameters. Furthermore, obesity was an additional risk factor for high IMT and smoking was an additional risk factor for high IMT and high PS. In contrast, in women, obesity, DL, or IFG was an additional risk factor for high IMT, high PS, or high baPWV, respectively. The risk factors for IMT, PS, and baPWV differ in in men and women. The management for atherosclerotic risk factors on early stage should be considered in terms of gender-specific risk factors.