Certain useful pharmaceutical agents carry a high risk of embryopathy. The US Food and Drug Administration (FDA), in cooperation with drug manufacturers, has established pregnancy prevention programs (PPPs) to reduce the incidence of birth defects for thalidomide (STEPS [System for Thalidomide Education and Prescribing Safety]) and isotretinoin (iPLEDGE) but not for other teratogenic drugs in clinical use. These programs are complex and raise important concerns regarding privacy, the clinician-patient relationship, and convenience of medical care. Furthermore, pregnancies continued to occur in isotretinoin-exposed females during the first full year of the iPLEDGE program. We review the design and application of STEPS and iPLEDGE and consider the ethical issues raised by the introduction of these programs. The goal is to eliminate birth defects caused by teratogenic agents, without making procedures so onerous that they result in restricted access to useful agents. Confidentiality must be maintained, and the rights of disadvantaged populations and individuals with special religious concerns must be protected. Informed consent must be complete and include all risks of treatment, including risks of contraceptive methods. All teratogenic agents should be covered by PPPs, which then must be no more burdensome than requirements that have existed for many years for other controlled substances.