With the advances in technical skills, management of postoperative complications and improvements in immunosuppressive drugs, liver transplantation is the standard treatment for many patients with chronic liver disease. Today, shortage of donor organs seems to be the major limiting factor for the application of liver transplantation. This review focuses on five issues that are challenging to clinical practice of liver transplantation and relevant to gastroenterologists. These include living donor liver transplantation, recurrent viral hepatitis, non-heart-beating donors, hepatocellular carcinoma, and ABO incompatible liver transplantation. Living donor and non-heart beating donor transplantations were initiated as a solution to increase the donor organ pool and it is expected that there will be an increase in the number of these donors. Recurrent hepatitis C and hepatocellular carcinoma following liver transplantation are among major problems and ongoing research in these diseases may lead to better outcomes in these recipients.