The purpose of the present study was to characterize histopathological lesions in primary biliary cirrhosis (PBC) and to assess the relationship between histopathological lesions and biochemistry. Liver biopsies of 252 patients with PBC were investigated. A laboratory database was established. Histopathological characterization was performed. Relationships between detailed histopathological features and biochemistry were calculated statistically. Combining the data, a PBC group, consisting of an anti-mitochondrial antibody (AMA)-positive and -negative subgroup, and an overlap group were defined, with a female preponderance of >90% and higher activity of aspartate aminotransferase (AST) in the overlap group. Histopathological changes were characteristic in >80%. Periductal concentric fibrosis, lobular granuloma formation and steatosis were frequently remarkable. Correlations were found between alanine aminotransferase activity and modified hepatitis activity index in the overlap group and the AMA-positive group. A positive significant relationship was demonstrated between mean AST activity and portal fibrosis for the AMA-positive group. A highly significant positive link was seen between mean concentration of bilirubin and stage of fibrosis. Biochemistry reflects only in part the degree of severity of histopathological lesions in PBC. Histopathology indicates comorbidity in a high percentage of patients.