OBJECTIVES: A case-referent study with 261 matched pairs was carried out in 8 hospitals of Comunidad Valenciana, Spain, to assess the relation between occupational exposure to pesticides and selected congenital malformations. In this paper, the results concerning paternal exposure are presented. METHODS: The parents of the case patients and the referents were interviewed to collect information about exposure to pesticides and potential confounding variables. Detailed information on direct involvement in the handling of pesticides was collected for the interviewees involved in agricultural activities during a previously defined period in relation to conception and pregnancy. Exposure data were reviewed by 2 experts who assigned ordinal scores for the probability and intensity of exposure to pesticide classes and active ingredients. RESULTS: The dichotomous analysis of exposure (absent, present) yielded some increased risks, although not statistically significant, for aliphatic hydrocarbons [adjusted odds ratio (adjusted OR) 2.05, 95% confidence interval (95% CI) 0.62-6.80], inorganic compounds (adjusted OR 2.02, 95% CI 0.53-7.72), and glufosinate (adjusted OR 2.45, 95% CI 0.78-7.70), and a significant association for pyridil derivatives (adjusted OR 2.77, 95% CI 1.19-6.44). The analysis based on the experts' scores (2 levels of exposure) showed some consistent associations for these compounds. CONCLUSIONS: This research indicates a possible risk of congenital malformations for paternal exposure to some pesticides, notably, pyridils, aliphatic hydrocarbons, inorganic compounds, and glufosinate. It did not find an increased risk for paternal exposure to pesticides in the classes of organophosphates, carbamates, organochlorines, chloroalkylthio fungicides and organosulfurs. These findings warrant further investigation.