Worker’s early detection and aggravation measures of lifestyle-related diseases are promoted using the medical checkup by the Ministry of Health, Labour and Welfare and the Health Insurance Union. For workers over 40 years old, the specific medical checkup is conducted to prevent lifestyle-related diseases such as metabolic syndrome, and it is checked blood pressure, blood sugar, lipids, waist circumference and so on. However, it is not easy to understand annual change whether it has improved or deteriorated as a whole. Therefore, we examined a system that combines comprehensive health score and factor visualization using 3 years data of male workers’medical checkup in the Health Insurance Union. As a result, we applied the Mahalanobis distance to judge the health score comprehensively and the three-dimensional mapping of hypertension, hyperglycemia and hyperlipidemia factors extracted from factor analysis, and visualized the transition trend.