A 39-year-old HIV-infected woman developed signs and symptoms of obstructive jaundice and cholestasis. Serological tests were positive for cytomegalovirus (CMV) infection. There was no evidence of AIDS cholangiopathy in ultrasonography or magnetic resonance cholangiopancreatography (MRCP). A liver biopsy revealed marked ductopenia and the patient was diagnosed with vanishing bile duct syndrome, thought to be secondary to CMV infection as a result of profound immunosuppression. To the best of our knowledge, this is the first reported case of vanishing bile duct syndrome diagnosed in a patient with HIV/AIDS.