A method provides fully autonomous patient matching by entities of a federated healthcare system. The method includes receiving an electronically formatted query for a patient from an autonomous healthcare entity in a federation of healthcare entities. The query includes at least an identifier of the entity, a unique patient identifier of the patient generated by the entity, and demographics of the patient. The method further includes searching a federated master patient index stored in master patient index storage for an entry likely to correspond to the patient. The method further includes identifying an entry for the patient. The method further includes updating the identified entry to include at least the identifier of the entity, the unique patient identifier of the patient generated by the entity and the demographics.