Fetal structural anomalies have an impact on fetal mortality and morbidity. Next Generation Sequencing (NGS) may be incorporated into clinical pathways for investigation of paediatric morbidity but also be used to delineate the prognosis of fetal anomalies. This paper reviews the role of NGS in the investigation of fetal malformations, the literature defining the clinical utility, the technique most commonly used and potential promise and challenges for implementation into clinical practice. Prospective case selection with informative pre-test counselling by multidisciplinary teams is imperative. Regulated laboratory sequencing, bioinformatic pathways with potential variant identification and conservative matching with the phenotype is important.