Multiple evidence support the prenatal predisposition of autism spectrum disorder (ASD). Nevertheless, robust data about abnormalities in fetuses later developing into children diagnosed with ASD are lacking. Prenatal ultrasound is an excellent tool to study abnormal fetal development as it frequently used to monitor fetal growth and identify fetal anomalies throughout pregnancy. We conducted a retrospective case-sibling-control study of children diagnosed with ASD (cases); their own typically developing, closest-in-age siblings (TDS); and typically developing children from the general population (TDP), matched by year of birth, sex and ethnicity to investigate the association between ultrasonography fetal anomalies (UFAs) and ASD. The case group was drawn from all children diagnosed with ASD enrolled at the Azrieli National Center of Autism and Neurodevelopment Research. Fetal ultrasound data from the fetal anatomy survey were obtained from prenatal ultrasound clinics of Clalit Health Services (CHS) in southern Israel. The study comprised 659 children: 229 ASD, 201 TDS, and 229 TDP. UFAs were found in 29.3% of ASD cases vs. only 15.9% and 9.6% in the TDS and TDP groups (aOR = 2.23, 95%CI = 1.32-3.78, and aOR = 3.50, 95%CI = 2.07-5.91, respectively). Multiple co-occurring UFAs were significantly more prevalent among ASD cases. UFAs in the urinary system, heart, and head&brain were the most significantly associated with ASD diagnosis (aORUrinary =2.08, 95%CI = 0.96-4.50 and aORUrinary = 2.90, 95%CI = 1.41-5.95; aORHeart = 3.72, 95%CI = 1.50-9.24 and aORHeart = 8.67, 95%CI = 2.62-28.63; and aORHead&Brain = 1.96, 95%CI = 0.72-5.30 and aORHead&Brain = 4.67, 95%CI = 1.34-16.24; vs. TDS and TDP, respectively). ASD females had significantly more UFAs than ASD males (43.1% vs. 25.3%, p = 0.013) and a higher prevalence of multiple co-occurring UFAs (15.7% vs. 4.5%, p = 0.011). No sex differences were seen among TDS and TDP controls. ASD fetuses were characterized by a narrower head and a relatively wider ocular-distance vs. TDP fetuses (ORBPD = 0.81, 95%CI = 0.70-0.94, and aOROcular-Distance = 1.29, 95%CI = 1.06-1.57). UFAs were associated with more severe ASD symptoms. Our findings shed important light on the abnormal multiorgan embryonic development of ASD and suggest fetal ultrasonography biomarkers for ASD.