Objective We present and defend ethically justified guidelines for pharmacologic research that involves pregnant women. Study design We explain the ethical concept of the fetus as a patient and identify its ethical implications for the design and conduct of pharmacologic research that is intended to benefit pregnant women. Results This concept justifies criteria for the initiation of early-phase clinical investigation, the initiation of controlled trials, the use of placebo control subjects, the stopping of randomized controlled trials, the determination of when an experimental intervention should be regarded as standard of care, and research that involves adolescents. The informed consent process should be shaped by the pregnant patient's obligation to take in to account her beneficence-based obligations to a fetal patient. Selection criteria should not be based on abortion preference. And, physicians are justified ethically in referring pregnant women to trials. Conclusion The concept of the fetus as a patient plays an essential role in the ethically justified design and conduct of pharmacologic research in pregnant women.