Growing understanding in recent years about the prevalence and diversity of mitochondrial DNA mutations in human diseases has prompted a need for a simple screening method. We designed multiplex mutation-specific PCR, in which mutant DNAs were selectively amplified, for the 3243 (A to G) and 8344 (A to G) mutations. This method was simple and sensitive. We detected bands corresponding to the mutations in 1 and 2% mixtures of the 3243 and 8344 mutations respectively. Mutation-specific PCR is useful for detecting mutant mitochondrial DNA in peripheral blood, where its ratio to wild type DNA is sometimes too small to be detected by conventional assay, and for large scale screening to uncover a hitherto unknown relationship between mitochondrial DNA mutations and certain diseases.