Introduction: Rural-urban health inequities, exacerbated by deprivation and ethnicity, have been clearly described in the international literature. To date, the same inequities have not been as clearly demonstrated in Aotearoa New Zealand despite the lower socioeconomic status and higher proportion of Māori living in rural towns. This is ascribed by many health practitioners, academics and other informed stakeholders to be the result of the definitions of 'rural' used to produce statistics. Aims: To outline a protocol to produce a ‘fit-for-health purpose’ rural-urban classification for analysing national health data. The classification will be designed to determine the magnitude of health inequities that have been obscured by use of inappropriate rural-urban taxonomies. Methods: This protocol paper outlines our proposed mixed-methods approach to developing a novel Geographic Classification for Health. In phase 1, an agreed set of community attributes will be used to modify the new Statistics New Zealand Urban Accessibility Classification into a more appropriate classification of rurality for health contexts. The Geographic Classification for Health will then be further developed in an iterative process with stakeholders including rural health researchers and members of the National Rural Health Advisory Group, who have a comprehensive ‘on the ground’ understanding of Aotearoa New Zealand's rural communities and their attendant health services. This protocol also proposes validating the Geographic Classification for Health using general practice enrolment data. In phase 2, the resulting Geographic Classification for Health will be applied to routinely collected data from the Ministry of Health. This will enable current levels of rural-urban inequity in health service access and outcomes to be accurately assessed and give an indication of the extent to which older classifications were masking inequities.