Anti-ganglioside antibodies are principally associated with autoimmune peripheral neuropathies. The most thoroughly studied disorder is the acute paralytic disease, Guillain-Barré syndrome (GBS) in which IgG autoantibodies against gangliosides arise following acute infections, notably Campylobacter jejuni enteritis. Additionally, chronic autoimmune neuropathies are associated with IgM antibodies directed against many glycolipids including gangliosides.

Anti-parietal cell antibodies (APCA) are an advantageous tool for screening for autoimmune atrophic gastritis (AAG) and pernicious anemia (PA). The target for APCA is the H+/K+ ATP-ase. It has been demonstrated, that APCA target both, the alpha, and beta subunits of the proton pump, although the major antigen is the alpha subunit.

Several markers for CD with a progressive diagnostic accuracy have been identified over the years, but only three of them, i.e. anti-tissue transglutaminase (anti-tTG), anti-endomysial (EmA) and anti-deamidated gliadin antibodies (DGP) are currently assessed in the daily clinical practice.

Basement membranes form an anatomic barrier that contains connective tissue. They are composed of type IV collagen, laminin and proteoglycans. Anti-basement membrane antibodies bind to the non-collagen site of the α 3 chain of type IV collagen. A group of renal diseases, pulmonary diseases and perhaps others affecting different organs have long been associated with the presence of antibodies directed against glomerular basement membrane (GBM), alveolar basement membrane and tubular basement membrane.

Anti-histone antibodies (AHAs) make their appearance in a number of systemic autoimmune diseases including systemic lupus erythematosus (SLE) and drug-induced lupus erythematosus (DILE). Although being known for over 50 years, they are poorly studied and understood. There is emerging evidence for their use in predicting clinical features of SLE, diversifying their clinical use. AHAs, however, are probably less prevalent in DILE than once thought owing to a move away from older DILE drugs to modern biological agents which do not appear to elicit AHAs.

Diagnosis of AIG is supported by the detection of gastric autoantibodies. Antiparietal cell antibodies (APCAs) are antibodies against gastric proton pump and are detected in approximately 90% of patients with PA. Anti-intrinsic factor antibodies (AIFAs) target proteins necessary for vitamin B12 absorption and are present in approximately 80% of patients with PA.

Anti-mitochondrial antibodies (AMA) are directed against the E2 subunits of the 2-oxo acid dehydrogenase complexes (PDC-E2) and are the typical biomarkers of primary biliary cholangitis (PBC). AMA are directed towards the pyruvate dehydrogenase multi enzyme complex (PDC-E2) subunit, which represents an epithelial specific autoantigen for PBC.

Antibodies against antigens found in the central nervous system have been evidenced in several neurological diseases. The most well-known are associated with paraneoplastic neurological diseases (Anti-Hu, Yo, Ri amphiphysin, Tr, CV2 and Ta antibodies). Some of these antibodies are specific for certain types of cancer or neurological syndromes and are highly useful diagnostic tools for the clinician. They have contributed to the hypothesis that these paraneoplastic neurological syndromes involve autoimmune cross reactions between tumoral and nervous system antigens.

Antineutrophil Cytoplasmic Antibody (ANCA)-Associated Vasculitis (AAV) is an autoimmune vasculitis that mainly includes Granulomatosis with Polyangiitis (GPA), Microscopic Polyangiitis (MPA), and Eosinophilic Granulomatosis with Polyangiitis (EGPA).

Anti-neutrophil cytoplasmic antibodies (ANCA) directed to proteinase 3 (PR3) represent highly established markers for patients with ANCA-associated vasculitis (AAV). PR3-ANCA have also demonstrated utility in the management of inflammatory bowel disease (IBD). More specifically, PR3-ANCA discriminate individuals with ulcerative colitis (UC) from Crohn's disease (CD) patients and are associated with disease severity, activity, and treatment non-response.