To optimise the health and cost benefits of Australia’s immunisation program, accurate data are required about how well the program is performing. Currently, this information is derived from stand-alone databases about vaccine coverage (the Australian Childhood Immunisation Register) and several separate databases about the occurrence of vaccine preventable diseases. We aim to link these datasets, for a cohort of children in Western Australia and New South Wales, to enable more accurate and detailed studies on the relationship between vaccination uptake, timeliness of vaccination, and development of disease, particularly in specific at-risk populations who may experience a higher burden of infection.