Mato Grosso is the largest agricultural producer and the largest national consumer of pesticides in Brazil. Maternal exposure to pesticides in the periconceptional period has been associated with increased risk of congenital malformations. This article aims to analyze the association between the use of pesticides and congenital malformations in cities with highest exposure to pesticides in Mato Grosso. It was a case-control study conducted with 219 live births with congenital malformations and 862 live births. The average use of pesticides was estimated in the prior and subsequent trimester to the date of fertilization and throughout the periconceptional period per city, month and year of use. Subsequently, these measures were quartilized and transformed into indicator-type (dummy) variables, attributing an exposure level for each interquartile interval. Bivariate and multivariate logistic regression analysis was conducted. Significant associations were observed (p < 0.05) in the third (OR = 1.66, 95% CI 0.98 to 2.79) and fourth quartile (OR = 1.88, 95% CI 1.09 to 3.24) of the post-fertilization period and the fourth quartile (OR = 2.04, 95% CI 1.17 to 3.56) throughout the periconceptional period. Maternal exposure to pesticides was associated with higher incidence of congenital malformations.