In the last decade, legislation on accounting harmonization and external audit readiness made public healthcare organizations devote increasing attention to the development of Internal Control Systems. Internal Auditing function (henceforth, IA) was frequently established and regarded as an opportunity to systematize and provide assurance upon the whole Internal Control System. This study is aimed at analyzing how the IA function has been implemented and developed in the Italian National Health Service. The empirical analysis relies on case study methodology and presents two of the most relevant experiences settled respectively in the Regional Health Services of Veneto and Emilia-Romagna. The study examines and compares: IA roles, types of audit, IA process, organizational variables, and internal auditors characteristics. Results show the existence of two distinct implementation modes, highly influenced by contextual factors, but also characterized by interesting similarities. These findings may provide a useful reference point for the establishment and implementation of the IA function in other regions.