Objectives: This study examined the association between certain paternal occupational exposures during the periconceptional period and the risk of congenital malformations. Materials and Methods: A case-control study was carried out from December 2009 to April 2010; on 242 congenital malformation cases and 270 controls. Paternal occupational exposure to certain workplace hazards was assessed by a detailed questionnaire to evaluate the occupational exposure for both fathers and mothers including pesticides, solvents, welding fumes, lead, working with video display terminals (VDTs) and computer monitors. In addition, the questionnaire assessed the presence of other risk factors such as consanguinity, smoking and history of any maternal diseases during the pregnancy with the child. Results: The results revealed that the odds of having a child with congenital malformation was higher (P < 0.01) if the father was occupationally exposed to pesticides (OR: 3.42, 95% CI: 1.97-5.92), solvents (OR: 5.63, 95% CI: 2.77-11.42), or welding fumes (OR: 2.98, 0.99-8.54) during the periconceptional period. However, consanguinity (OR: 1.91, 95% CI: 1.25-2.92) was a risk factor of developing congenital malformations among offspring. Conclusion: Control of workplace exposures and adherence to threshold limit values of those hazards should be adopted to minimize the risk of developing congenital malformations among offspring.