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Background Congenital Heart Disease represents the most frequent fetal malformation. The lack of prenatal identification of congenital heart defects can have adverse consequences for the neonate, while a correct prenatal diagnosis of specific cardiac anomalies improves neonatal care neurologic and surgery outcomes. Sonographers perform prenatal diagnosis manually during the first or second-trimester scan, but the reported detection rates are low. This project’s primary objective is to develop an Intelligent Decision Support System that uses two-dimensional video files of cardiac sweeps obtained during the standard first-trimester fetal echocardiography (FE) to signal the presence/absence of previously learned key features. Methods The cross-sectional study will be divided into a training part of the machine learning approaches and the testing phase on previously unseen frames and eventually on actual video scans. Pregnant women in their 12–13 + 6 weeks of gestation admitted for routine first-trimester anomaly scan will be consecutively included in a two-year study, depending on the availability of the experienced sonographers in early fetal cardiac imaging involved in this research. The Data Science / IT department (DSIT) will process the key planes identified by the sonographers in the two- dimensional heart cine loop sweeps: four-chamber view, left and right ventricular outflow tracts, three vessels, and trachea view. The frames will be grouped into the classes representing the plane views, and then different state-of-the- art deep-learning (DL) pre-trained algorithms will be tested on the data set. The sonographers will validate all the intermediary findings at the frame level and the meaningfulness of the video labeling. Discussion FE is feasible and efficient during the first trimester. Still, the continuous training process is impaired by the lack of specialists or their limited availability. Therefore, in our study design, the sonographer benefits from a second opinion provided by the developed software, which may be very helpful, especially if a more experienced colleague is unavailable. In addition, the software may be implemented on the ultrasound device so that the process could take place during the live examination. Trial registration The study is registered under the name „Learning deep architectures for the Interpretation of Fetal Echocardiography (LIFE)”, project number 408PED/2020, project code PN-III-P2–2.1-PED-2019. Trial registration: ClinicalTrials.gov, unique identifying number NCT05090306, date of registration 30.10.2020.