Healthy physicians are critical to the quality of care for patients. There is a common trend in Chinese societies seeking for medical treatments from Chinese medicine physicians. However, there are limited studies that investigated the health status for the Chinese medicine physicians. In this report, we used National Health Insurance Research database of Taiwan between 1998 and 2002 to compare the morbidities between Chinese medicine physicians and general population. The number of Chinese medicine physicians in this study is 6,143 (5,036 males with the mean age of 40.47 years and 1,107 females with the mean age of 36.24 years), and the number of the referent subjects is 24,576, randomly selected from the database matching by sex and age. We found that the Chinese medicine physicians have lower all-causes morbidity (86% vs. 95%, p < 0.001), except that female Chinese medicine physicians had significantly higher rates of complications of pregnancy, childbirth, and puerperium than female population. Such an exception might reflect a consequence of maternal age effect. The odds ratio between all causes and two comparison groups was 0.36 (95% CI: 0.33, 0.40), indicating that the Chinese medicine physicians have much lower disease risk. Higher education, better socioeconomic status, and good knowledge in medicine (possible self-treatment) may explain the observed differences. Among the Chinese medicine physicians, the morbidity rate of male subjects is lower than the female subjects (85.9% vs. 91.4%, p < 0.001). This study will provide the helpful information in guiding future investigations about health hazards to the practice of Chinese medicine.