Mitochondrial DNA (mtDNA) mutation was investigated in a hepatoma patient using a polymerase chain reaction (PCR) and an in situ hybridization technique. Biotin-labeled probes for the subunit m of cytochrome c oxidase revealed differences in the in situ hybridization. A PCR assay using biopsied and microdissected tissues showed that common deletion (4,977 bp) was more pronounced in the cancer region than in the normal parts of the same patient. These results suggest that mtDNA deletion might be associated with tumorigenesis in hepatoma.