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Human data on the teratogenicity of selective serotonin reuptake inhibitors (SSRIs) are limited. We examined the association between SSRI use during early pregnancy and the risk of congenital malformations in the offspring.In a population-based cohort study from Denmark, we identified 1051 women who filled prescriptions for SSRIs from 30 days before conception to the end of the first trimester; of those, 453 filled the prescription during the second or third pregnancy month. We included 150,780 women with no SSRI prescriptions as a reference cohort. Drug use data were extracted from prescription databases. Data on congenital malformations and potential confounders were extracted from hospital discharge registries and the National Birth Registry.The 150,780 women with no SSRI prescriptions gave birth to 5112 (3.4%) children with congenital malformations. The 1051 women with SSRI prescriptions any time during early pregnancy gave birth to 51 (4.9%) children with congenital malformations. The corresponding adjusted relative risk (aRRs) was 1.34 (95% confidence interval = 1.00–1.79). The 453 women with prescriptions during the second or third month of pregnancy gave birth to 31 (6.8%) children with congenital malformations. The corresponding aRR was 1.84 (1.25–2.71).We found an increased risk of congenital malformations after exposure to SSRIs in early pregnancy. It is unclear whether the effects were causal or due to factors related to the underlying disease. There was no evidence that the association was specific to particular malformations.