Tissue injury in primary biliary cirrhosis is thought to be mediated by immune mechanisms. Various Class II antigens of the major histocompatibility complex are associated with autoimmune diseases and their differing clinical manifestations. Thus, the aim of this study was to examine the relationship between primary biliary cirrhosis, its clinical manifestations and serologically defined Class II antigens (HLA-DR and HLA-DQ). Typing for these antigens was performed in 114 primary biliary cirrhotic patients and 171 controls by lymphocytotoxicity. There was a 6-fold increase in the frequency of HLA-DRw8 in primary biliary cirrhosis as compared to controls [30.1 vs. 4.7% (p < 0.0001)]. In contrast, HLA-DR5 had a decreased frequency in primary biliary cirrhosis as compared to controls [9.8 vs. 25.2% (p < 0.02)]. We examined the relationship between Class II antigens and the following prognostic indicators in primary biliary cirrhosis: serum bilirubin; 24-hr urine copper; serum albumin; prothrombin time; platelet count; ascites, and histologic stage (I to IV). Patients who are positive for HLA-DRw52 (n = 82) had a 2-fold increase in serum bilirubin compared to those who are negative (n = 32) for this antigen (p < 0.05). Conversely, patients who are positive for HLA-DR2 had less than half the serum bilirubin values of those negative for this antigen (p < 0.02). In conclusion, we found different Class II antigens to be associated with a prognostic indicator in primary biliary cirrhosis (serum bilirubin), while HLA-DRw8 is strongly associated with the disease itself. These data suggest that determining Class II antigens may be important in predicting the course and clinical expression of primary biliary cirrhosis.