Previously reported associations of a common polymorphism near melanocortin-4 receptor (MC4R) gene (rs17782313) with BMI/obesity were inconsistent, especially in East Asia, and the associations of the polymorphism with serum lipid levels have not been fully elucidated. This study evaluated the association between rs17782313 and obesity-related traits and serum lipid levels in the general Japanese population. A total of 2,035 subjects (aged 35-69 years, 1,024 males and 1,011 females) enrolled in the Japan Multi-Institutional Collaborative Cohort (J-MICC) Study. We examined the associations between near MC4R polymorphism (rs17782313) and obesity-related traits [height, weight, body mass index (BMI), weight change from 20 years old], serum lipid levels (triglycerides, total and HDL-cholesterol), and intake of nutrients (total energy and macronutrients). Polymorphism of rs17782313 (minor C allele) was positively associated with serum triglyceride levels (P for trend = 0.020) adjusted for age and sex. Analysis using a general linear model revealed that the number of minor C alleles was positively associated with serum triglyceride levels after adjustment for age, sex, and potential confounders (P for trend = 0.004). Statistical significance did not change after further adjustment for total energy intake and BMI. There was no significant association between rs17782313 and obesity-related traits including BMI. Interactions between rs17782313 and sex, BMI, or total energy intake for triglyceride levels were not significant. To our knowledge, this study demonstrated for the first time that rs17782313 was associated with serum triglyceride levels in Asian population. Further studies are needed to confirm this result.