AIM: To investigate the function of the prot ein tyrosine kinase of focal adhesion kinase subfamily gene, the gene regulation and the signaling pathway related to ventricular septal defect during heart dev elopment. METHODS: The ALK3 downstream genes were screened usin g microarray. The ALK3 downstream genes was identified using RT-PCR and real tim e quantitative RT-PCR.RESULTS: It was found that the protein ty rosine kinase of focal adhesion kinase subfamily gene was up-regulated 3.7 fold in the 11.5 days embryonic heart of cardiac- specific deletion of ALK3 mice. CONCLUSION: The protein tyrosine kinase of focal adhesion kinase subfamily possibly is a regulatory factor in bone morphogenetic protein signalin g pathway and may be related with the development of ventricular septal defect.