ObjectiveTo evaluate the frequency of structural congenital anomalies (CAs) in the midwest of Brazil and its association with maternal risk factors.MethodsThis was a prospective, observational, case-control study based on a hospital population. Pregnant women attended at a fetal medicine service in Brazil were analyzed in the period from October 2014 to February 2016.A total of 357 pregnant women were included, 223 of whom had fetuses with structural anomalies (group case), and 134 of whom had structurally normal fetuses (control group). The clinical history was made previous to prenatal consultation, and the diagnosis of the structural CA was performed through ultrasound.ResultsA frequency of 64.27% (n= 223) of pregnant women with fetuses with structural anomalies was observed. The most frequent structural CAs were those of the central nervous system (30.94%), followed by anomalies of the genitourinary system (23.80%), and, finally, by multiple CAs (16.60%). The background of previous children with CAs (odds ratio [OR]: 3.85;p= 0.022), family history (OR: 6.03;p= < 0.001), and consanguinity between the progenitors (OR: 4.43;p= 0.034) influenced the occurrence of structural CA.ConclusionThe most frequent CAs are those of the central nervous system, followed by those of the genitourinary system, and then multiple anomalies. The maternal risk factors that may have influenced the occurrence of structural CA were previous children with CA, family history, and consanguinity among the parents.