The diagnosis of autoimmune diseases invariably requires the detection of autoantibodies, in association with suggestive clinical symptoms, which develop in relation to the involvement of specific or nonspecific organ systems. Many autoantibodies have well‐defined target antigens and can be detected with high analytical sensitivity. Autoantibodies act as biomarkers helping to diagnose disease subsets and monitor autoimmune diseases. The indirect immunoflorescence technique remains the hallmark of diagnosis, but is increasingly being replaced by enzyme immunoassays or multiplexed assays. Comprehensive methods of analysing multiple antibodies simultaneously using multiplex assays are being developed for routine use in the diagnosis, study of the specificity and pathophysiology of autoimmune diseases and the development of antigen specific therapies. Clinical proteomics offers the opportunity to identify new disease biomarkers to help in diagnosing and managing autoimmune diseases.

Key Concepts:

• The diagnosis of autoimmune diseases depends on clinical suspicion and supportive immunological tests.
  
• Test for autoantibodies only when there is a clinical suspicion of autoimmune disease as weakly positive ANAs may be present in the normal healthy population.
  
• Autoantibodies can be used in diagnosis, monitoring of disease flares and remission, sub‐setting disease, evaluating severity and prognosis.
  
• The indirect immunoflorescence technique remains the hallmark of diagnosis, but is increasingly being replaced by enzyme immunoassays or multiplexed assays.
  
• Multiplexed immunoassays support the identification of multiple autoantibodies from a single determination simultaneously without having to do follow up testing.
  
• Multiplex assays are advantageous as a single test may be used for both screening and determining antibodies of clinical significance.
  
• Clinical proteomics offers the opportunity to identify new disease biomarkers in body fluids, cells and tissues to help diagnose diseases.