To obtain the risk estimates of autism spectrum disorder (ASD) in the offspring exposed to serotonin reuptake inhibitors (SSRI) in utero, we performed systematic review and meta-analysis of relevant studies. Five case-control and three cohort studies were eligible for the analysis. The SSRI group had significantly higher risk of ASD than the SSRI non-exposed group (pooled OR 1.45, 95% CI 1.15-1.82). In the subgroup analyses, however, the risk of ASD was similar between the SSRI group and other antidepressants group (pooled OR 1.14, 95% CI 0.67-1.96). Furthermore, when the analysis was confined to those born to the women with psychiatric disorders, the SSRI group did not show an increased ASD risk (pooled OR 0.96, 95% CI 0.57-1.63) compared to non-exposed groups. In conclusion, SSRI use in pregnancy is associated with an increased risk of ASD in the offspring, but maternal psychiatric condition is a major confounding factor.