Abstract： Objective To detect the gene defect of mitochondrial DNA(mtDNA) from skeletal muscles in 2 patients with chronic progressive external ophthalmoplegia (CPEO).Methods After extraction of mtDNA, Southern hybridization was performed after restrictive digestion by PvuⅡ, EcoRI, Hind Ⅲ, and SacI. Then, we carried out polymerase chain reaction(PCR) and the enzyme digestion of the PCR products. Finally, mtDNA sequencing was done by automatic DNA sequence analyzer. Results In case 1, a 5 kb deletion was found by Southern blot analysis and PCR. And dosage analysis showed a heteroplasmic change with 44% mtDNAs deleted. In case 2, PCR plus restriction endonuclease PvuⅡ digestion demonstrated a mutation which was confirmed by DNA sequencing to be a single base substitution (T→C) inducing a novel PvuⅡ site around 10909 on mtDNA sequence. The laser image analyzer measurement revealed the mutation was almost homologous (99.4% mutant).Conclusions In case 1, a 5 kb deletion found in mtDNA is called "common deletion" according to the literature. In case 2, a novel PvuⅡ site was found. It seems to be a de novo point mutation affecting ND4 in published CPEO research and is first reported in Chinese population. This point mutation does not induce an amino acid(Phe) change according to the published human mitochondrial genetic code as well as the mtDNA sequence. Whether it affects the translation efficiency or transportation of signals between mitochondrial and nuclear genome needs further studies.