: Type three progressive familial intrahepatic cholestasis (PFIC3) is a rare disorder which is caused by defect in bile secretion and presents with intrahepatic cholestasis, usually in infancy and childhood. It is autosomal recessive in inheritance. The defect is in adenosine triphosphate binding cassette, sub-family B, member 4 (ABCB4) gene encoding multidrug-resistant protein 3 (MDR3). MDR3 is a p-glycoprotein (pGp) which is a phospholipid translocator and responsible for biliary secretion of phospholipids, predominantly phosphatidylcholine (PC). A case of infant with cholestasis was reported in the article and explored for underlying pathogenesis. A 9-month-old girl, who had recovered from cytomegalovirus (CMV) infection, had elevated bile acids and gamma-glutamyl transpeptidase (GGT) for seven months with unknown reason. She was examined for hereditary and metabolic disease-associated genes. A heterozygous mutation of ABCB4 gene was found. PFIC3 was suspected. It was considered that patient with heterozygous ABCB4 gene mutation had residual gene expression and a relatively low level of MDR3 proteins. Without risk factors, the biliary secretion in the patient would be normal. But CMV infection further down regulated the gene expression, disturbing the bile secretion, leading to cholestasis. After antiviral therapy, oral ursodeoxycholic acid (UDCA) and glutathione were administered and her liver tests improved gradually. Therefore, patients with persistent cholestasis of unknown reasons may undergo genetic sequencing to identify whether there is mutation of genes related to cholestatic liver disease. CMV infection may play a role in persistent cholestasis of the patient with ABCB4 gene variance.