Jaundice in patients with AIDS can be a result of diverse conditions ranging from opportunistic infections to drug-related hepatotoxicity. With the advent of antiretroviral therapy (ART), the prevalence of AIDS cholangiopathy as a cause of jaundice has decreased; on the other hand, ART-related hepatotoxicity has become one of the commonest causes of jaundice in these patients. AIDS cholangiopathy is a rare condition of extrahepatic biliary obstruction in patients with advanced HIV infection, usually due to opportunistic infections. Vanishing bile duct syndrome (VBDS) is an acquired disorder characterized by progressive destruction and loss of interlobular bile ducts causing intrahepatic cholestasis. Herein, we report co-occurrence of fatal cytomegalovirus (CMV)-induced VBDS along with papillary stenosis, as a component of AIDS cholangiopathy, which to the best of our knowledge has not been documented earlier. This is perhaps the third case of VBDS in a patient with AIDS, and the second in association with CMV infection. VBDS in AIDS has a poor outcome, and liver transplantation may be considered only in a suitable candidate.