Waist circumference (WC) is measured for the assessment of abdominal obesity, whereas carotid intima-media thickness (IMT) is a marker of preclinical atherosclerosis. The relationship between WC and carotid IMT in the general population is not fully understood. In this study, we examined 1,182 subjects (658 men and 524 women, 62.3 ± 11.7 years on average) who underwent voluntary health check-ups and sought to determine the optimal cut-off value of WC for predicting carotid IMT thickness. Receiver operating characteristic curve analysis of WC was utilized to predict high carotid IMT (defined as carotid IMT ≥ 1.1 mm). We determined that the appropriate WC cut-off value was a WC ≥ 79 cm for men and women. There was a statistically significant difference in the prevalence of high carotid IMT between WC ≥ 79 cm and WC < 79 cm in both men and women. However, multivariable logistic regression analysis demonstrated that the WC category was independently associated with high carotid IMT in men, but not in women. Our study indicates that the optimal cut-off value of WC to identify preclinical atherosclerosis may be lower than the current Japanese diagnostic criteria for metabolic syndrome (MetS) in both men and women. Compared to women, the association between WC and preclinical atherosclerosis may be more pronounced in men.