The objective of this paper is to estimate the cost of obesity's contribution to the metabolic syndrome diseases in Taiwan. We used individual data from the Cardiovascular Disease Risk Factors Two-Township Study survey and medical use and expenditures data from the Bureau of National Health Insurance (NHI) of Taiwan. By adopting the prevalence-based and population attributable risk (PAR) approaches, direct costs of obesity for six kinds of obesity related metabolic syndrome diseases have been estimated. Comorbidities used in our analysis included ischemic heart diseases, congestive heart failure, cerebrovascular disease accident, diabetes, hyper-cholesterolaemia and hypertension. The results indicate that overweight and obesity are associated with a higher prevalence and costs of the metabolic syndrome related diseases. PAR increases as the obese [body mass index (BMI)] prevalence increases. About 4–9% of the costs of those diseases can be attributed to overweight (24 ≤ BMI < 27) and about 7–13% and 8–19% of such costs are attributable to the first and second degree obesity (27 ≤ BMI < 30 and BMI ≥ 30). The cost of obesity derived from the PAR and medical costs of metabolic syndrome diseases accounts for 2.9% of the national total healthcare expenditure. We therefore conclude that overweight and obesity have increased health costs and resulted in higher prevalence of and greater costs from metabolic syndrome related diseases in Taiwan. These findings provide important support for implementing obesity prevention programs in Taiwan.