Ethnic disparities in chlamydia infections in The Netherlands were assessed, in order to compare two definitions of ethnicity: ethnicity based on country of birth and self-defined ethnicity. Chlamydia positivity in persons aged 16-29 years was investigated using data from the first round of the Chlamydia Screening Implementation (CSI, 2008-2009) and surveillance data from STI centres (2009). Logistic regression modelling showed that being an immigrant was associated with chlamydia positivity in both CSI [adjusted odds ratio (aOR) 2·3, 95% confidence interval (CI) 2·0-2·6] and STI centres (aOR 1·4, 95% CI 1·3-1·5). In both settings, 60% of immigrants defined themselves as Dutch. Despite the difference, classification by self-defined ethnicity resulted in similar associations between (non-Dutch) ethnicity and chlamydia positivity. However, ethnicity based on country of birth explained variation in chlamydia positivity better, and is objective and constant over time and therefore more useful for identifying young persons at higher risk for chlamydia infection.