Objective To investigate the clinical phenotype and IRF6 gene mutation in two Chinese kindred with Van der Woude syndrome (VWS),and understand the mutations of IRF6 and suspicious mutation hotspots in Chinese people. Methods The peripheral blood of 24 members from two VWS families were collected and directly performed the polymerase chain reaction (PCR) for screening the coding region of IRF6 gene.The soft ware of mutation surveyor was used to analysis the sequence. Results There were six VWS subjects in two families,5 (83.3%) patients had cleft lip and palate;5 (83.3%) patients had lip fistula.The results of IRF6 gene sequencing showed,six patients had mutations of IRF6 gene in 24 family members.The c.1234C>T heterozygous mutation was detected in 3 patients of family 1.In family 2,3 patients were carrying c.1210G> A heterozygous mutations.The other members of the families were wild type (wt/wt) for IRF6. Conclusions Based on these findings,the spectrum of mutations in IRF6 associated with VWS is extended.Genetic testing showed that cosegregated with the disease mutation.The identification of the role of IRF6 in VWS may help us to study any possible genotypephenotype relationship by combining molecular genetics.The mutations will play important role in genetic analysis and prenatal diagnosis of VWS.The ultrasound easily missed cleft palate,genetic testing can compensate for the lack of prenatal ultrasound.