Objective To explore the correlation between mutations in the promoter region of TBX1 gene and conotruncal heart defects. Methods A total of 621 children with conotruncal heart defects were recruited. Multiplex ligation-dependent probe ampliifcation (MLPA) was used to detect the copy numbers of chromosomal region 22 q 11 . 2 . Children with 22 q 11 . 2 deletion were excluded. Polymerase chain reaction ampliifcation (PCR) and gene sequencing were applied to analyze promoter region of TBX 1 (-2000 ..+1 ) in 605 children with conotruncal heart defects without 22 q 11 . 2 deletion and 588 healthy children. Bioinformatics software was used to predict and analyze the function of the variable loci. Results There were mutations in the promoter region of TBX 1 gene in children with conotruncal heart defects, including 3 single nucleotide polymorphisms (SNP) sites and 7 rare loci. The incidence of mutation was 1 . 7%. The analysis of 7 rare loci by AliBaba 2 . 1 to showed that 3 of them may inlfuence the combination of trans-acting factors and cis-acting elements of the promoter of TBX 1 gene. Conclusion The mutation in the TBX 1 promoter region may be related to the occurrence of conotruncal heart defects.