Objective · To explore the correlation between variants located in 3' untranslated regions (3'UTR) of NOTCH1 and JAG1 genes and conotruncal heart defects (CTD). Methods · Six hundred CTD children without 22q11 deletion and three hundred healthy children were enrolled in this hospital-based case-control study. Variants located in the 3'UTR regions of NOTCH1 and JAG1 genes were detected by high-throughput sequencing. The accuracy of the variants were verified by PCR and Sanger sequencing. Online software PicTar, TargetScan and microRNA.org were used to make functional predictions. Results · One mutation and three SNPs were found in the 3'UTR of NOTCH1. Three mutations and six SNPs were found in the 3'UTR of JAG1. The genotypic distributions of two SNPs (rs3840074 and rs8708) located in JAG13'UTR between CTD group and the controls were statistically significant (both P<0.05). Results of prediction showed that all the four mutations and two meaningful SNPs could bind to microRNA. Conclusion · The variants located in 3'UTR regions of NOTCH1 and JAG1 genes may be related to the occurrence of CTD.