The action plan sets out how the Scottish Government aims to help people suffering from rare conditions such as cystic fibrosis and Huntington's disease.
Patients and health experts were consulted for the report, which outlines potential improvements to prevention, diagnosis and early intervention.
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It highlights the need for more research to develop the understanding and treatment of rare diseases, as well as improved training programmes to help health and social workers better identify conditions.
A rare disease is defined as a life-threatening or debilitating condition affecting fewer than five people in 10,000. There are thought to be between 6,000 and 8,000 known rare diseases.
Public Health Minister Michael Matheson said: "What this report demonstrates is that although these diseases are individually rare, the sheer number of different conditions means that the total number of people affected is surprisingly large. That is why we have drawn up this implementation plan, so we can really focus our efforts on improving services for people who are living with rare diseases."