Several autoimmune diseases (primary and secondary) can affect the liver and bile ducts. While the exact cause remains unclear, early diagnosis is crucial to prevent complications. The authors' main objective is to review imaging features of various autoimmune disorders, including autoimmune hepatitis, primary biliary cholangitis, primary sclerosing cholangitis, immunoglobulin G4 (IgG4)-related diseases, and drug-induced autoimmune injury. These disorders are chronic inflammatory conditions causing destruction of hepatocytes or cholangiocytes, destruction of the latter potentially leading to cholestasis and associated ductopenia. Complications related to untreated autoimmune disorders include sequelae of chronic liver failure or cirrhosis, such as portal hypertension and ascites. Neoplasms arising in the setting of cirrhosis related to autoimmune diseases include hepatocellular carcinoma, cholangiocarcinoma, and gallbladder cancer. As these autoimmune disorders of the liver and biliary tract characteristically involve bile ducts and cause cholestasis, MRI or MR cholangiopancreatography (MRCP) is the preferred imaging modality, given its ability to provide excellent anatomic details of the bile ducts and demonstrate changes in the liver parenchyma. Understanding the imaging appearance of each of the autoimmune disorders affecting the liver and biliary tract allows a particular diagnosis to be suggested. Imaging studies often provide the first clues to an autoimmune disorder of the liver and bile ducts, enabling early diagnosis to halt progression and prevent complications. In addition, imaging studies are also useful for monitoring progression of disease, assessing treatment response, and detecting complications during follow-up.