Objective To investigate the keratin 9 gene mutation in epidermolytic palmoplantar keratoderma (EPPK) and its relationship with clinical manifestations. Methods Three Chinese pedigrees with EPPK were studied. Polymerase chain reaction (PCR) was performed to amplify the seven exons encoded by keratin 9. Denaturing high-performance liquid chromatography (DHPLC), DNA sequencing and allele-specific PCR were used to reveal the sequence variation in the PCR products. Results An insertion-deletion mutation in the exon 1 of keratin 9 497delAinsGGCT, was revealed in all 3 EPPK families, resulting in the keratin 9 change from tyrosine166 to tryptophan and leucine (Y166delinsWL). Allele-specific PCR confirmed that the mutation was not a commonly seen polymorphism, but a novel mutation which has not been reported in The Human Intermediate Filament Mutation Database (http://www.interfil.org). Conclusions A new keratin 9 gene mutation, 497delAinsGGCT, is found in these Chinese EPPK pedigrees, which may be the genetic basis of EPPK.