The most common mutations present in both cell lines were involved in the following genes: D-loop, 12S rRNA, 16S rRNA, ND1, ND2, ND4, ND5, COI, COIII, ATPase6 and CYTB. Among these variations, ten alterations were identified as novel in HCC cell lines, six in Huh-7 and four in HepG-2. Here, MT-CO3 is linked to hepatocellular carcinoma.