INTRODUCTION: Exposure to pesticides is a known risk to human health. The association between parental exposure and congenital malformations is described. OBJECTIVE: We sought to study the association between exposure to pesticides and congenital malformations in newborns who were born at the Regional Hospital of Encarnación in Itapúa, Paraguay. METHODS: This was a prospective case and control study from March 2006 to February 2007. A case was defined as a newborn who was born with congenital malformations, and a control case was defined as a newborn of the same gender who was born immediately after and was found to be healthy. The exposure to pesticides was considered along with other risk factors that are known to cause congenital malformations. RESULTS: The cases (52) and controls (87) were analyzed. The average number of births per month was 216. The risk factors that were significantly associated were living near fumigated fields (odds ratio [OR]: 2.46 [95% confidence interval (CI): 1.09–5.57]; P < .02), having pesticides in the house (OR: 15, 35 [95% CI: 1.96–701.63]; P < .003), direct or accidental contact with pesticides (OR: 3.19 [95% CI: 0.97–11.4]; P < .04), and history of family malformations (OR: 6.81 [95% CI: 1.94–30.56]; P < .001). The other risk factors known to cause malformations did not have statistical significance. CONCLUSIONS: The results show an association between the exposure to pesticides and congenital malformation in newborns who were born at the Regional Hospital of Encarnación. Future studies are required to confirm these findings.