Recent reports have focused on the difficulty in differentiating autoimmune hepatitis from chronic hepatitis C due to the high prevalence of anti-HCV in autoimmune hepatitis. The aim of this study was to identify clinical, biochemical, and serological variables that would help distinguish these two diseases. Pretreatment clinical and biochemical variables were compared from 17 patients with steroid-responsive autoimmune chronic active hepatitis and 62 patients with chronic hepatitis C. Serum samples from these patients were tested for autoantibodies and for anti-HCV by first- and second-generation ELISA, recombinant immunoblot assay, and HCV RNA by polymerase chain reaction. Patients with autoimmune hepatitis were more likely to be symptomatic (94% vs 47%, P < 0.005) and jaundiced (76% vs 0%, P < 0.005) at the time of referral. Anti-HCV was found in 53% of patients with autoimmune hepatitis, but only two were positive by immunoblot assay and only one of these had detectable HCV RNA. Antinuclear antibody (ANA) was detected in 21% of patients with chronic hepatitis C, although usually at a lower titer than in autoimmune hepatitis (geometric mean titer = 1:160 vs 1:500, P < 0.003). Patients with chronic hepatitis C who were ANA positive were older than those who were ANA negative, although there were no other differences in clinical or biochemical features between these groups. In particular, there was no difference in response rate to antiviral therapy. Thus, autoantibodies are frequently found in chronic hepatitis C, especially in older subjects, but appear to be clinically insignificant. Anti-HCV is frequently present in autoimmune hepatitis but is rarely confirmed by tests of higher specificity.(ABSTRACT TRUNCATED AT 250 WORDS)