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A case of low-GGT cholestasis associated to USP53 gene mutation in a Brazilian child is described. Transient jaundice and hypocholia started at age 10 days old. Liver enzymes, total bilirubin and total bile acids were elevated at presentation. During follow-up, he developed cholelithiasis treated with cholecystectomy, and an intracranial hemorrhage resolved with full recovery. At last evaluation at 18 months of age, he was not jaundiced and had normal liver tests, but suffered from moderate pruritus despite treatment with rifampicin and ursodeoxycholic acid. A genetic study revealed novel homozygous mutations c.1687_1688delinsC p.Ser563Profs*25 in the USP53 gene. His parents carried the same heterozygous mutation in the USP53 gene.