Viral infections of horses have significant impact on animal welfare and can lead to huge economic losses. One of the first early signs of a viral infection is the development of fever and to at this early step be able to identify the agent behind the infection would lead to rapid and correct treatment and also allow for the implementation of proper biosecurity measures to stop further spread. However, aetiology of fever and also some of the clinical features that may follow, e.g. neurological disorders, often remains undiagnosed. This study will use viral metagenomics to investigate the cause behind fever cases in Swedish horses as well as behind neurological disorders of horses from Sweden and from the other Nordic countries. The methodology allows us to identify all viruses present in an investigated clinical sample. Thus we hope that the knowledge gained from this project can help to further improve equine health and control the spread of these viral infections.