The growing popularity of traditional medicine (TM) is reflected in the increasing trend for its use worldwide. Many people are turning to use TM as a complementary or integrative treatment. The aim of this study is to present the first nationwide report describing the use of TM in two countries (South Korea and Taiwan). To present the TM utilization patterns between South Korea and Taiwan, we analyzed data from the National Health Insurance cohorts in each country, each of which has approximately one million inhabitants. In total, 261,478 (25.5%) of 1,025,340 people in South Korea and 260,529 (26.8%) of 970,866 people in Taiwan used TM services at least once under the National Health Insurance in 2011. Using multivariable logistic regression, TM users in South Korea were significantly more likely to be female, 61-80 years of age and individuals with a high income, and those in Taiwan were significantly more likely to be female, 21-40 years of age and individuals with a middle income. The two countries showed similar utilization patterns in visit seasons. People visited TM clinics more frequently than TM hospitals in both countries. The most common TM treatment in South Korea was acupuncture, whereas in Taiwan, various powdered Chinese herbal preparations were the most commonly used treatment. The most common diseases for people seeking TM services were musculoskeletal system and connective tissue diseases in South Korea and Symptoms, signs, and ill-defined conditions in Taiwan. According to the National Health Insurance database, about one fourth of the NHI beneficiaries of South Korea and Taiwan had TM use in 2011. Different TM utilization patterns existed between South Korea and Taiwan, which might be due to the differences in insurance coverage between the two countries.