The history of rare diseases remains largely unexplored, as their origins, prevalence, and social perception in past societies are poorly understood. Investigating rare diseases in archaeological and prehistoric contexts requires a clear definition, yet modern epidemiological criteria cannot be applied due to preservation issues and limited sample sizes. Genetically determined rare diseases caused by spontaneous mutations can be considered relatively stable over time, while multifactorial diseases must be interpreted within their specific archaeological context. Defining rare diseases as a group increases their visibility and relevance in archaeological research. Diagnosing rare diseases in skeletal remains is challenging due to incomplete preservation and the absence of laboratory data, making awareness of rare pathological features essential to avoid missed diagnoses. Standardized documentation and transparent data sharing are necessary to enable comparative studies beyond isolated case reports. The Digital Atlas of Ancient Rare Diseases (DAARD) provides a framework for publishing cases in accordance with FAIR principles, including clear documentation of sampling and analytical methods. The study of rare diseases in bioarchaeology allows, for the first time, the investigation of their long-term morphological and genetic development. This approach offers new insights into the medical and social history of rare diseases, supports their visibility, and fosters collaboration between researchers and patient communities.