Background: Food insecurity, an issue also affecting developed countries, is associated with different negative outcomes. Particularly in pregnant women, a vulnerable population group, it has a double burden, as it affects both the woman and her child. Food insecurity has been associated with low birth weight and shorter gestational age, but there is less evidence on the association with fetal structural anomalies. Aim: To fill this gap, a study will be conducted to examine if pregnant women in a condition of food insecurity have a higher risk for fetal structural anomalies. Methods: A case-control study will be conducted in three centers. Cases will be pregnant women (>18 years old) diagnosed with a fetal structural anomaly during the prenatal ultrasound examination of the II–III trimester, while controls will be pregnant women (>18 years old) with a negative result for fetal structural anomaly at the II–III trimester prenatal ultrasound examination. The exposure of interest will be food insecurity during the last 12 months, measured using the validated Household Food Insecurity Access Scale. A dedicated questionnaire will be given to women after they sign the informed consent form. Summary: Finding a positive association between food insecurity in pregnant women and fetal structural anomalies could be the first step towards screening for it among pregnant women and designing policies that could mitigate this condition. Lowering food insecurity could prevent a certain number of fetal structural anomalies, leading to fewer negative pregnancy outcomes and health problems during childhood and adulthood.