Biliary tract brush specimens are fast becoming the method of choice in the evaluation of patients who present with biliary tract strictures. Although the specificity is high, sensitivity rates for the detection of malignancy are generally low on cytological sampling. New liquid-based preparations and ancillary tests have emerged with the intent of addressing this issue. This review focuses on the current schemata used in the diagnosis of biliary tract lesions and the current available modalities which aid in the diagnosis of cholangiocarcinoma.