Mitochondrial respiratory chain disorders (MRCD) are a large group of disorders that can affect any organ besides muscles or the central nervous system. We report two children who presented with neonatal cholestasis and progressive cirrhosis, who subsequently developed hepatocellular carcinoma (HCC). This suggests a particular risk of degeneration in these patients and the importance of a regular screening for secondary liver cancer. Suggestion of HCC should lead to early liver transplantation, which was successful without tumor recurrence in the two patients.