BACKGROUND Cytomegalovirus (CMV) infection is a common infection in liver transplant recipients, which is related to chronic rejection and biliary complications. It is often diagnosed based on serum CMV-DNA or CMV pp65. To our knowledge, this is the first report of the successful treatment of occult CMV cholangitis in a pediatric liver transplantation (LT) recipient. CASE SUMMARY A 7-mo-old baby girl received LT due to biliary atresia and cholestasis cirrhosis. At 1 mo following LT, the patient suffered from aggravated jaundice with no apparent cause. As imaging results showed intrahepatic and extrahepatic bile duct dilatation, the patient was diagnosed with biliary complications and percutaneous cholangiography and biliary drainage was performed. However, there was little biliary drainage and her liver function deteriorated. CMV-DNA was isolated from the bile with the surprising outcome that 3 x 10(6)copies/mL were present, whereas the CMV-DNA in serum was negative. Following antiviral therapy with ganciclovir, she gradually recovered and bilirubin decreased to normal levels. During the 4-year follow-up period, her liver function remained normal. CONCLUSION Bile CMV sampling can be used for the diagnosis of occult CMV infection, especially in patients with negative serum CMV-DNA and CMV pp65. Testing for CMV in the biliary tract may serve as a novel approach for the diagnosis of cholestasis post-LT. Timely diagnosis and treatment will decrease the risk of graft loss.