Surveillance of rare diseases in children is an important aspect of public health. Rare diseases affect thousands of children worldwide. The Canadian Paediatric Surveillance Program (CPSP) has been in existence since 1996, and provides an innovative means to undertake paediatric surveillance and increase awareness of childhood disorders that are high in disability, morbidity, mortality, and economic costs to society, despite their low frequency. Traditionally, CPSP used manual paper-based reporting on a monthly basis, which although had an impressive response rate, it had inherent longer processing times and costs associated with it. The article below describes an innovative web-based system that enables seamless reporting from participants across the country providing a quick, reliable and simple mechanism for the users to submit data while yielding better data quality, timeliness and increased efficiencies. The development of such a system represents a significant advancement in the public health informatics area, building capacity for seamless and rapid data management for national surveillance.