The aim of this study was to expose the background for proposing core indicators for children’s health and well-being at the municipal level in Greenland; to define criteria for relevant and scientifically sound indicators; to propose a set of such indicators; to give data on their distribution, and compare the outcomes between different types of municipalities. The indicators were drawn from actual knowledge of children’s health and experiences reported in international studies. They were based on goals from the National Public Health strategy and the UN Convention on the Rights of the Child. A set of 24 indicators were identified in 4 domains (demographic and socio-economic conditions; health status and well-being; determinants of health, risk, and protective factors; and health systems and health policy). Additional indicators were proposed for later implementation, most of these lack available data. Data revealed large differences between municipalities. In general, remote communities have the most unfavourable socio-demographic and health conditions. At the same time, larger communities’ access to health care services is more favourable. A consequence is that the health care system unintentionally contributes to the increasing health gap between privileged and less privileged children. A comprehensive strategy is need to guarantee equitable health standards for all Greenlandic children and that reaches far beyond the aims stated in the present national public health programme.