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Background  Race and ethnicity classification systems have considerable implications for public health, including the potential to reveal or mask inequities. Given increasing “super-diversity” and multiple racial/ethnic identities in many global settings, especially among younger generations, different ethnicity classification systems can underrepresent population heterogeneity and can misallocate and render invisible Indigenous people and ethnic minorities. We investigated three ethnicity classification methods and their relationship to sample size, socio-demographics and sexual health indicators.    Methods  We examined data from New Zealand’s HIV behavioural surveillance programme for men who have sex with men (MSM) in 2006, 2008, 2011, and 2014. Participation was voluntary, anonymous and self-completed; recruitment was via community venues and online. Ethnicity allowed for multiple responses; we investigated three methods of dealing with these:  Prioritisation ,  Single/Combination , and  Total Response . Major ethnic groups included Asian, European, indigenous Māori, and Pacific. For each classification method, statistically significant associations with ethnicity for demographic and eight sexual health indicators were assessed using multivariable logistic regression.    Results  Overall, 10,525 MSM provided ethnicity data. Classification methods produced different sample sizes, and there were ethnic disparities for every sexual health indicator. In multivariable analysis, when compared with European MSM, ethnic differences were inconsistent across classification systems for two of the eight sexual health outcomes: Māori MSM were less likely to report regular partner condomless anal intercourse using  Prioritisation  or  Total Response  but not  Single/Combination , and Pacific MSM were more likely to report an STI diagnosis when using  Total Response  but not  Prioritisation  or  Single/Combination .    Conclusions  Different classification approaches alter sample sizes and identification of health inequities. Future research should strive for equal explanatory power of Indigenous and ethnic minority groups and examine additional measures such as socially-assigned ethnicity and experiences of discrimination and racism. These findings have broad implications for surveillance and research that is used to inform public health responses.

Ethnicity classification systems for public health surveys: experiences from HIV behavioural surveillance among men who have sex with men