Vaccination has provided major benefits to the health of indigenous children in the face of continuing poorer socioe-conomic conditions but several issues have been identified for improvement. While indigenous children are vaccinated at high rates for the standard schedule vaccines, vaccination is more commonly delayed. Coverage for ‘targeted’ vaccines is substantially lower, and data on coverage for indigenous adolescents is non-existent. Improved identification of indigenous clients by immunisation providers and the expansion of the childhood register are required. The progressive removal of early-acting Haemophilus influenzae type b vaccines from schedules for indigenous children because of an international shortage raises the risk of disease re-emergence and highlights the need for vigilant surveillance including carriage. The expanded use of existing vaccines (influenza) and early adoption of new vaccines (higher valency pneumococcal conjugates) are needed to maximise benefits, in particular the potential to impact on non-invasive disease such as otitis media and non-bacteraemic pneumonia that are so prevalent in indigenous children.