Inflammatory disorders of the biliary tract present difficult diagnostic problems in liver needle biopsies. The aim of this study was to perform a detailed histologic analysis of liver biopsies from patients with biliary tract disorders, classify them by pattern of inflammation, and determine the accuracy of the histologic classification by clinical follow-up. Percutaneous liver needle biopsies from the surgical pathology files of UmassMemorial Healthcare (UMMHC) from 2000 to 2003 with a diagnosis suggesting a biliary tract process (n = 32) and four biopsies from cases with systemic non-biliary tract disorders were analyzed for multiple histologic features and classified as one of five patterns: acute cholangitis/pericholangitis (ACP), lymphocytic cholangitis (LC), granulomatous (G), ductopenia (D), or non-specific (NS). When compared to the "gold standard" diagnosis based on all clinical data, the concordance between the histologic classification and the clinical diagnosis was: 50% for ACP and bile duct obstruction; 77% for LC and immune-mediated cholangitis NOS; 100% for G and G cholangitis; 100% for D and idiopathic adulthood D; and 50% for NS and non-biliary tract disorders. Our findings suggest that classifying biopsies by pattern of injury is helpful in guiding the subsequent clinical work-up. ACP pattern correlates with bile duct obstruction, infection, and ischemia. LC correlates with serologic studies supporting immune-mediated processes. G pattern suggests further work-up for PBC, drug, tuberculosis, or sarcoidosis. D pattern establishes the clinical diagnosis. NS pattern includes cases of primary sclerosing cholangitis, which cannot be diagnosed by biopsy alone.