The evidence for the association between threatened abortion and birth defects is limited and inconsistent. This study examined this relation using data from the Shanghai Birth Defects Monitoring Program. A total of 1,013 cases of birth defects and an equal number of controls were analyzed. Our study showed that women with threatened abortion had a 50% higher risk of having a baby with birth defects compared with those without this complication, controlling for other factors (adjusted odds ratio = 1.5; 95% confidence interval = 1.1–2.1). Threatened abortion was generally related to defects of the urogenital system, heart and circulatory system, and musculoskeleton and limbs and was specifically associated with polydactyly, undescended testicle, and hypospadias.