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The objective of this research is to determine the prevalence and demonstrate the association between exposure to pesticides before and during the first trimester of gestation and the risk of congenital malformations in the cardiovascular, genitourinary, central nervous systems and malformations of the face, mouth, palate and extremities. Likewise, to identify whether the consumption of medications (anticonvulsants, antihypertensives, antiemetics and anticoagulants), history of alcoholism, drug use and severe anemia during the first trimester of gestation increases the risk of congenital malformation. The study design is observational, retrospective cross-sectional, analytical case-control study. The cases (n=57) were selected by non-probabilistic sampling and the controls (n=114) by simple random sampling from a hospital population in the Ica Region, during a 3-year period. Cases were defined as neonates with congenital malformations of the cardiovascular, genitourinary, centralnervous, digestive, face, mouth, palate and extremities systems; controls were newborns without the aforementioned malformations.