Van der Woude syndrome (VWS, OMIM 119300) is an autosomal dominant craniofacial disorder characterized by pits of the lower lip, hypodontia and cleft lip and/or cleft palate.The incidence of VWS is 1-3/30000, penetrance is 80-94%.Popliteal pterygium syndrome (PPS, OMIM 119500) is an autosomal dominant syndrome with clinical phenotype very similar to VWS. Besides the phenotypes similar to VWS, PPS patients may also have Popliteal pterygium, syndactyly or genitalia abnormality.Recently, Kondo et al. disclosed mutations of the interferon regulatory factor 6 (IRF6) gene in VWS and PPS patients, and therefore proved these two syndrome allelic diseases. To investigate the condition of pathogenic gene of VWS and PPS in China, and therefore facilitate the future research on IRF6 gene structure, function and signal transduction pathway, we imploied PCR and sequencing method to screen the possible mutations of IRF6 gene in four Chinese VWS families and one PPS family. Results:In VWS family I, a complete segregated transversion GCC to GTC (c.5C>T) was disclosed at codon 2 , with a predicted amino acid residue change A2V.In VWS family II, a complete segregated transversion CGC to TGC (C.16C>T) was disclosed at codon 6 , with a predicted amino acid residue change R6C.In VWS family III, a complete segregated transversion TGG to TGA (C.1137C