We previously reported anti-PCNA autoantibodies in sera from patients with chronic HBV and HCV infection. To analyse the antigenic regions on proliferating cell nuclear antigen (PCNA) that confer autoantibody binding in patients with chronic hepatitis B (HBV) and C (HCV) infection, eight constructs including one wild type PCNA, one mutant type Y114A_PCNA and six C- or N-terminal PCNA truncations were generated. Sera from 185 patients with systemic lupus erythematosus (SLE), 178 with chronic HBV and 163 with chronic HCV infection, and 68 healthy individuals were examined for the presentation of anti-PCNA antibodies by enzyme linked immunosorbent assay (ELISA). By ELISA, anti-PCNA positive sera from patients with SLE, chronic HBV and HCV infection preferentially recognized the wild type PCNA more than the mutant type Y114A_PCNA (P < 0.05). The inhibition of binding by purified full-length rPCNA proteins with anti-PCNA positive sera was shown to exceed 70%. The inhibition of binding by purified truncated rPCNA proteins with sera from patients with chronic HBV and HCV infection and SLE was shown to confer dominant binding in T(L2) and T(L3). Moreover, the higher frequency of inhibition by using T(L3) was found in patients with chronic HBV infection. These data indicate that anti-PCNA autoantibodies preferentially recognize C-terminal of PCNA in patients with chronic HBV infection and may also provide advanced understanding between viral infection and autoimmunity for further study.