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Background  New Zealand initiated HPV vaccination in 2008, and has attained 3-dose coverage of ~50 % in 12–13 year old girls. Due to the success of program initiatives in Māori girls, higher coverage rates of ~60 % have been achieved in this group. We have previously reported a benchmark overall pre-vaccination prevalence of oncogenic HPV infection in high grade cervical lesions in New Zealand. The current extended analysis provides separate pre-vaccination benchmark prevalence for Māori and non-Māori women.    Methods  The National Cervical Screening Programme Register (NCSP-R) was used to identify any woman aged 20–69 years of age with an index high grade cytology report from 2009–2011. Extended recruitment was performed until 2012 in clinics with a high proportion of Māori women. Ethnicity status was based on self-reported information by participating women through phone contact supplemented by recordings on the study questionnaire (the NCSP-R was not used to extract ethnicity status). A total of 730 women consented to participate and had a valid HPV test result; 418 of these had histologically-confirmed cervical intraepithelial neoplasia (CIN) 2/3 lesions (149 Māori, 269 non-Māori). The prevalence of any cervical oncogenic HPV infection, HPV16, and HPV18 was calculated in women with CIN2/3.    Results  In confirmed CIN2/3, the prevalence of any oncogenic HPV, HPV16 and HPV18 was 96 % (95 % CI:91–99 %), 54 % (95 % CI:46–63 %), 11 % (95 % CI:7–18 %) in Māori and 96 % (95 % CI:93–98 %), 54 % (95 % CI:48–60 %), 11 % (95 % CI:7–15 %) in non-Māori women, respectively. Age-specific patterns of infection for HPV16/18 in confirmed CIN2/3 differed between the two groups (P interaction  = 0.02), with a lower prevalence in younger  vs.  older Māori women (57 % in 20–29 years vs 75 % in 40–69 years) but a higher prevalence in younger  vs.  older non-Māori women (70 % in 20–29 years vs 49 % in 40–69 years); the difference in the age-specific patterns of infection for HPV16/18 was not significant either when considering confirmed CIN2 alone ( p  = 0.09) or CIN3 alone ( p  = 0.22).    Conclusions  The overall prevalence of vaccine-included types in CIN2/3 was similar in Māori and non-Māori women, implying that the long-term effects of vaccination will be similar in the two groups.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-015-1034-5) contains supplementary material, which is available to authorized users.

Pre-vaccination type-specific HPV prevalence in confirmed cervical high grade lesions in the Māori and non-Māori populations in New Zealand