Birth defects occur in about 3% of live-birth. The causes of birth defects varied, with 25% due to chromosome anomalies, 20% due to single gene disorders, 50% due to multifactorial (complex inheritance) diseases, and ~5% due to teratogen factors. With the development of new technologies, many previously unidentified clinical syndromes now have molecular answers. The first breakthrough in molecular testing in pediatric patients is the application of genome-wide high density oligonucleotide array comparative genomic hybridization (array CGH). It is a powerful technology that allows for the detection of DNA copy number changes that previously not detectable by conventional cytogenetic techniques. Compared with conventional cytogenetic techniques which only find anomalies in 5-10% of patients with multiple congenital anomalies or mental retardation, array CGH can answers 25-30% of patients. More recently, the next generation sequencing (NGS) technology is also applied to pediatric genetic disorders. Several disease-based NGS panels have been designed for the diagnosis of mitochondrial diseases, Noonan spectrum, skeletal dysplasia, and glycogen storage disease, etc. These NGS panels effectively decrease the efforts required for molecular testing in diseases with significant genetic heterogeneity. Furthermore, whole genome sequencing (WGS) and whole exome sequencing (WES) not only detect diseases with known etiologies, but also identify new genetic bases of diseases. Although WGS or WES are mostly on research bases currently, we believe that they will become the major molecular testing methods in the near future.