Background: The cost and economic burden of diabetes are a serious worldwide issue. In this study, we evaluated medical payments for persons diagnosed with diabetes and the factors that led to a person having diabetes to reduce its prevalence. Methods: A dataset containing 113,979 medical checkups and 3,671,783 monthly medical, dental, care-giving and pharmacy payment records of one health insurance society was used. The dataset contains information of normal and healthy persons. The sample period ran from April, 2013 to March, 2016. The medical payments for persons diagnosed with diabetes were calculated. The regression analysis was used to remove the effects of age and gender. The probit analysis was used to analyze the factors that led to a person having diabetes. Results: In 2.9% of cases, the person undergoing the checkup was diagnosed with diabetes, and the medical payments for these patients were 2.7 times as much as the average medical payment per person. This result did not change significantly even if age and gender were considered. The results of the probit analysis suggested that body mass index, high systolic blood pressure, low diastolic blood pressure, eating habits, physical activities, smoking, drinking alcohol and sleeping were important factors for diabetes. Conclusion: The diabetes might be a costlier disease than previously thought in Japan. By the estimation, 8% of all medical payments were made for these persons with diabetes, which is much higher than the result shown by national survey data. However, overall prevalence could be recused by efforts such as prevention of overweight and obesity.