Rare diseases in children account for disproportionate morbidity and mortality and are particularly demanding of both families and health resources. Surveillance may provide data on their epidemiology, aetiology, management and outcome and on the support requirements of affected children. Existing methods for rare disease surveillance include mandatory and voluntary notification schemes, which may be active or passive, hospital discharge databases and death certification data. The recent establishment of the Australian Paediatric Surveillance Unit has facilitated active, prospective, national case ascertainment by voluntary notification of selected rare conditions. Information obtained should enable estimation of incidence rates, evaluation of prevention and management strategies, extend data collected by existing methods and help estimate future health needs.