Worksite health promotion programs focusing on diet and lifestyle modification have been shown to improve health outcomes in workers. The purpose of this study was to investigate whether a 12-week worksite health promotion program shows different response of cardiovascular risk factors in subjects according to apolipoprotein E (Apo E) genotype and obesity level in 141 male Korean industrial workers. We hypothesized that the health changes of a 12-week intervention may not be the same within Apo E genotypes in nonobese and obese subjects. They received 5 face-to-face meetings based on their health profiles. In obese group carrying Apo E3 genotype, body mass index, body fat (%), waist circumference, waist-hip ratio, and systolic blood pressure were decreased, as well as intakes of energy (P = .000) and carbohydrate (P = .005). High-density lipoprotein cholesterol (P = .004) level was improved in individuals with the Apo E2 genotype. These beneficial effects were only observed in individuals with the Apo E2 or Apo E3 genotype. Multiple linear regression revealed that obesity was strongly correlated with waist circumference (P = .002), plasma total cholesterol (P = .037), and changes in dietary cholesterol intake (P = .011) in individuals with the Apo E3 genotype, whereas only changes in dietary fat intake (P = .044) was correlated in those with the Apo E4 genotype. Overall, the results of this study suggest that a health promotion program can be a useful method of improving cardiovascular risk factors and dietary intake in industrial workers with certain genotypes only. Therefore, further research is needed to develop a tailored, long-term worksite health promotion program based on genetic background.