The World Health Organization Family of International Classifications (WHO-FIC) includes three reference classifications: the International Statistical Classification of Diseases and Related Health Problems (ICD), the International Classification of Functioning, Disability, and Health (ICF), and the upcoming International Classification of Health Interventions (ICHI). The WHO has combined the content of these three classifications into a single WHO-FIC Foundation. However, as these classifications evolved independently, duplicate or related concepts may be represented differently across them. These challenges necessitate an investigation into how to eliminate redundancies, resolve conflicting content, ensure consistent representation, and clarify the relationships among concepts. This study aimed to identify areas of overlap, inconsistency, and duplication within the reference classifications, with the goal of analyzing the nature of the related entities and recommending areas and methods for further harmonization. A multi-step process was implemented: topics were inventoried, and based on this inventory; a typology was created to characterize the overlaps, analyze the nature of the related entities, and suggest methods for harmonizing each type of overlap. The project identified over 100 specific areas of overlap and demonstrated that when semantic overlap exists, it is vital to remove redundancies and create logically consistent combined hierarchies. Further discussions are needed to address harmonization approaches, prioritization, and resource allocation. In addition, use cases are needed to establish the criteria and principles for content harmonization. The WHO-FIC Network must now decide on the nature of the desired harmonized Foundation and its implications for the ICD-11, ICF, and ICHI update process.