Purpose To describe the ethnic differences in central corneal thickness (CCT) in population-based samples of ethnic Bai, Yi and Han people living in rural China. Methods 6504 adults (2119 ethnic Bai, 2202 ethnic Yi and 2183 ethnic Han) aged 50 years or older participated in the study. Each subject underwent standardized ocular examinations and interviewer-administered questionnaires for risk factor assessment. CCT was measured for both eyes using an ultrasound pachymeter. Regression and principal component analysis were performed to examine the relationship of ethnicity and other factors with CCT. Results The mean CCT readings were 536.4 +/- 34.2 mu m in ethnic Bai, 532.1 +/- 32.1 mu m in ethnic Yi and 529.6 +/- 32.7 mu m in ethnic Han adults (P<0.001), respectively. There was a decreasing trend of mean CCT with increasing age across all ethnic groups. In multivariate linear regression models, increasing CCT was associated with younger age (P<0.001), male gender (P<0.001), Bai (P<0.001) or Yi (P<0.001) ethnicity, greater body mass index (P<0.001), higher systolic blood pressure (P<0.001), greater corneal curvature (P<0.001), deeper anterior chamber (P < 0.001), and thicker lens (P<0.001). Ethnicity contributed significantly to presence of thin cornea (60%; P<0.001) compared with other factors. CCT had similar impact on intraocular pressure readings across all ethnic groups. Conclusions This study of more than 6500 multiethnic participants demonstrates significant ethnic variations in CCT, with Han ethnicity having the thinnest cornea compared with ethnic minorities. These data are essential to guide future multiethnic clinical trials on CCT-related ocular conditions such as glaucoma.