A genetic predisposition has been suggested in primary sclerosing cholangitis (PSC) and primary biliary cirrhosis (PBC). The aim of the study was to evaluate human leukocyte antigen (HLA) frequencies and HLA associations in Finnish PSC and PBC patients. The relative frequencies of HLA-A,-B, and-DR antigens were compared between patients with PSC (n=50), or PBC (n=89), transplanted due to end-stage liver disease, and healthy members in the Finnish bone marrow donor registry (n=10000). Prevalence differences, prevalence ratios and the associated large-sample significance probabilities (2-sided P-values) and 95% confidence intervals were calculated.We found a strong positive association between PSC and HLA-B8 and-DR3, and a weak positive association between HLA-A1 and PSC. HLA-DR3 also had a weak positive association with PBC, and a weak negative association between HLA-DR5 and PBC was found. In conclusion, HLA-B8, and-DR3 are susceptible for progressive liver disease in PSC, and HLA-DR3 may also be susceptible for disease progression in PBC. HLA-DR5 may be protective against severe PBC.