简介：AbstractCongenital heart disease (CHD) is the most common birth defect worldwide. In recent years, the widespread application of innovative molecular diagnostic technologies in clinical scenarios has obviously increased the molecular diagnostic yields of CHD, providing evidence-based guidance for medical decision-making. These molecular diagnostic technologies include chromosome microarray analysis, targeted sequencing, exome sequencing, and genome sequencing. Furthermore, high-throughput sequencing technology has performed excellently in the clinical molecular diagnosis of CHD. This review provides an overview of the current technology and applications in the molecular diagnosis of CHD. The unmet issues and future directions in adapting novel genomic testing technologies to the molecular diagnosis of CHD in clinical settings are also addressed.