Aniridia is a paradigm of the challenges posed to healthcare systems by childhood-onset rare diseases. The care of children with rare diseases presents peculiar aspects of complexity, due to the chronicity of these conditions and their disability spectrum, with different types of impairments and different severity levels, both within the same disease and the same patient across life. Recently, the provision of more comprehensive and effective care has been the aim of health policies specifically addressed to rare disease patients. The experience carried out in this field by the Veneto region (4.9 million inhabitants, north-east of Italy) is presented. An information system, accessed by all the different health professionals involved in patients’ care, has been developed. The system, adopted so far in other seven Italian Regions, allows patients’ recording, treatments’ prescription and provision and the formulation of care plans, according to the individual health care needs’ profile. The process of information sharing can effectively reduce the fragmentation of the care provided to these children and their families by a multiplicity of actors, medical and non-medical ones. Furthermore, it can ease the transition from paediatric to adult care, an emerging crucial issue in the care of children presenting special care needs, as children with aniridia.