To determine if shared genetic risk factors for autoimmune liver disease af
fect clinical manifestations, we evaluated 271 patients and 92 normal subje
cts by DNA-based techniques. Genetic risk factors were intermixed in all co
nditions, and frequency varied according to disease type. DR4 distinguished
autoimmune hepatitis (P = 0.0002) and primary biliary cirrhosis (P = 0.004
) from primary sclerosing cholangitis. DR52 distinguished primary sclerosin
g cholangitis from autoimmune hepatitis (P = 0.0007) and primary biliary ci
rrhosis (P = 0.00007) and DR3 distinguished autoimmune hepatitis (P = 0.002
) and primary sclerosing cholangitis (P = 0.0005) from primary biliary cirr
hosis. Only the occurrence of DR4 in primary sclerosing cholangitis was low
er than in normal subjects (P = 0.02). Patients with mixed genetic risk fac
tors did not have distinctive features or manifestations of hybrid conditio
ns. We conclude that patients with shared genetic risk factors do not have
characteristic features nor do they have overlap syndromes. DR4 may be prot
ective against primary sclerosing cholangitis.