Smith-Lemli-Opitz syndrome (SLOS) is an autosomal recessive disease caused by a mutation in the 7-dehydrocholesterol reductase gene (DHCR7) on chromosome 11, which leads to 7-dehydrocholesterol reductase enzyme defects. This results in the building up of toxic by-products of cholesterol production in the blood and the nervous system. All this affects the growth and development of human body systems. We presented a case of a fetus of a pregnant woman with a high-risk pregnancy after IVF. The patient was referred for a fetal karyotype test, which showed a male sex (46, XY). This woman was referred to our centre for fetal heart evaluation. Based on our protocol established at the Department of Prenatal Cardiology of the Institute of the Polish Mother’s Health Centre in Lodz, our examination starts with obstetrical screening, including ultrasound fetal gender evaluation. At this point of examination, the fetus presented ambiguous genitalia and fetal polydactyly. The fetal echocardiographic examination revealed atrioventricular septal defect. The presence of ambiguous genitalia and atrioventricular septal defect allowed us to suspect SLOS. As a result, further diagnostic steps were suggested, and the diagnosis was confirmed. The family chose comfort care with no postnatal intervention and planned the next pregnancy with another donor. We would like to underline the importance of a detailed ultrasound protocol before fetal echocardiographic examination for its proper interpretation.