BackgroundMost fetal defects are associated with genetic and environmental causes, among them, exposure of pregnant women to intensive pesticide use. Agribusiness is the economic basis of the state of Mato Grosso, the largest consumer of pesticides of all Brazilian states. The objective of this study was to investigate the association between past parental exposure to pesticides and the occurrence of congenital malformations in children in Mato Grosso, Brazil.MethodsThis hospital-based case–control study was conducted in Cuiabá, the capital of Mato Grosso, from March to October 2011. Data was collected in all public, private, and health plan referral hospitals that provide care for pregnant women in the state of Mato Grosso and were situated in Cuiabá. Cases were children under 5 years of age with congenital malformations classified in Chapter XVIII of the International Classification of Diseases-10 and controls were children within the same age range, without congenital malformations, treated at the same hospitals. Malformation-related data was obtained from the patients’ medical records. Socioeconomic data and information about parental exposure to pesticides were obtained in an interview with the mother using a standardized questionnaire. We conducted multivariate logistic regression to assess the relation between parent report of past pesticide use and congenital malformations. We also assessed effect modification to verify whether low maternal education level modified the association between exposure and our outcome.ResultsWe observed positive effect modification of the association of paternal past exposure to pesticide and congenital malformation in the offspring by maternal education for mothers with low educational level (OR = 8.40, 95 % CI 2.17–32.52), father’s work related to farming (OR = 4.65, 95 % CI 1.03–20.98) and paternal past exposure to pesticides (OR = 4.15, 95 % CI 1.24–13.66).ConclusionThese findings provide further evidence that paternal exposure to pesticides, especially when associated with a low maternal education level, may be related to higher rates of fetal malformation in Mato Grosso, Brazil.