Clomiphene citrate (CC) is the oldest drug used to regulate the process of ovulation. Considering the great use of CC over the last 40 years, it is important to understand the possible risks associated with its use. The aim of this review was to evaluate the possible teratogenic effects of CC, analyzing results obtained from animal and human studies. The pharmacokinetics of CC and possible mechanisms involved in teratogenesis are examined. Fetal exposure to CC is possible due to the long half-life of CC and its metabolites. Alarming data have emerged from animal studies, although controversial results come from human studies. There is some evidence regarding a possible association of CC exposure and fetal malformations, mainly neural tube defects and hypospadias, which would require further investigation in order to allow safer use of this useful drug.