Privacy incursions in the clinical care of substance abusing pregnant women have gained lay and professional attention recently as the result of a high-profile Supreme Court finding in Ferguson vs City of Charleston et al. In March, 2001 the Supreme Court determined that nonconsensual drug screening of pregnant women by clinicians in a public hospital violated the women's Fourth Amendment rights to be secure against unreasonable search and seizure. Coercive or punitive policy approaches to perinatal substance abuse are often based on mistaken assumptions about the nature of addiction and the outcomes of punitive interventions. Much attention has been given to efforts to criminalize pregnancy for drug using women, and civil laws are also coming under increasing scrutiny. Although no state has passed a law criminalizing pregnancy and drug use, an estimated 250 women in more than 30 states have been prosecuted around the country on theories of "fetal abuse." A growing number of states (eighteen to date) have amended their civil child welfare laws to address specifically the subject of a woman's drug use during pregnancy. No one has examined how these laws and social policies could affect research that includes pregnant and parenting women; women (and their families) who stand to lose a great deal should their drug use be brought to the attention of child welfare or criminal justice authorities. We examine the adequacy of current protective mechanisms, such as federal certificates of confidentiality, in protecting research subjects (and investigators) who may be subject to punitive civil or criminal sanctions. We determine that current protective mechanisms may be insufficient to protect research subjects and that investigators and IRB members are often ignorant of the risks imposed by punitive policy approaches to perinatal substance abuse or fall prey to the same mistaken assumptions that inform punitive policies. We conclude that investigators and IRB members have a moral responsibility to understand local, state and national policies and laws governing perinatal substance abuse. Investigators and IRB members should balance the harms of punitive interventions against the protections that may, or may not be afforded to prospective research subjects as well as the prospective benefits, individual and social, of the research. In situations where criminal or punitive policies are in effect, investigators and IRB members should consider whether adequate protections can be achieved. In the context of inadequate protections, potential risks to prospective research subjects and their families may outweigh the individual or social benefits that accrue from the research. Clinical researchers are professionally obligated to work toward amending laws and policies that are not in the best interests of prospective research subjects.