BACKGROUND: Data on the safety of selective serotonin-reuptake inhibitors (SSRIs) in pregnancy are inconsistent. We examined associations between SSRI use during early pregnancy and risk of congenital malformations in infants. METHODS: Set in Northern Denmark, our population-based prevalence study included 216,042 women who had a live birth after the 20th week of gestation. We compared the prevalence of malformation in infants born to women who redeemed at least one SSRI prescription during early pregnancy with the prevalence in infants born to women who redeemed no SSRI prescriptions during their pregnancies. Drug use data were extracted from prescription databases, while data on congenital malformations were obtained from the National Registry of Patients. RESULTS: The 2,062 women with SSRI prescriptions during early pregnancy gave birth to 105 (5.1%) infants with malformations, while the 213,712 women with no SSRI prescriptions gave birth to 7,449 (3.5%) infants with malformations. SSRI use was associated with an increased risk of malformations overall (odds ratio [OR] = 1.3; 95% confidence interval (CI): 1.1-1.6) and cardiac malformations (OR = 1.7; 95% CI: 1.1-2.5). For specific SSRIs, we found an increased risk for septal defects associated with sertraline. CONCLUSIONS: We found little overall association between use of SSRIs during pregnancy and congenital malformations, but our findings suggest an association between maternal SSRI use in early pregnancy and cardiac malformations which could be causal.