The diagnosis of PBC includes liver function tests (determination of alkaline phosphatase, aspartate transaminase and alanine transaminase), the determination of serum lipids, screening for anti-mitochondrial antibodies (AMA) and anti-nuclear antibodies (ANA) and the differentiation from other chronic inflammatory diseases of the liver, such as chronic viral hepatitis, autoimmune hepatitis or primary sclerosing cholangitis.

The detection of AMA is of great importance in the diagnosis of PBC. Antibodies against the M2 antigen are the most sensitive and specific diagnostic marker. These antibodies can be found in 94% of PBC patients. High-titer anti-M2 antibody seropositivity is an important tool in the diagnosis of PBC and a very powerful predictor of future development of PBC in patients without significant liver function disorders or symptoms suggestive of cholestatic diseases. Besides AMA, ANA may also be found in about one third of patients with PBC by indirect immunofluorescence. Promyelocytic leukaemia (PML) proteins and Sp100, which generate a nuclear dot pattern in IIFT, and two components of the nuclear pore complex (gp210 and p62) that have been specifically associated with a perinuclear pattern have been identified as specific ANA target antigens in PBC.