Ventricular septal defect (VSD) is the most frequent congenital cardiac malformations. Amniotic fluid (AF) contains a higher abundance of biological compounds that could reflect fetal health information. The aims of our study were to construct a competitive endogenous RNA (ceRNA) network based on AF-derived exosomal ncRNAs. We conducted whole transcriptome profiling in six pairs of AF-derived exosomes from VSD fetuses and matched healthy controls. A total of 1252 differentially expressed (DE) mRNAs, 256 DE-miRNAs and 1090 DE-lncRNAs were found to be significantly altered in the VSD group. We constructed a ceRNA regulatory network including 46 mRNAs, 11 miRNAs and 47 lncRNAs. The expression level of 6 hub RNAs were validated using qRT-PCR. In conclusion, AF-derived exosomal VSD-related ceRNAs provide a basis for a better understanding of the role of ncRNAs in the pathogenesis and mechanisms of VSD, which may lead to the discovery of potential diagnostic biomarkers for fetal VSD. • We confirmed the presence of exosomes in the amniotic fluid (AF). • Our study provided the first systematic profiling of the whole transcriptome in AF-derived exosomes of VSD fetuses. • Our study constructed a ceRNA network which might play a modulating role in the pathogenesis of VSD. [ABSTRACT FROM AUTHOR]