The vast majority of HIV-infected women are of childbearing potential, so issues surrounding reproduction and mother-to-child transmission of the virus are critical in the management of this population. Optimal antiretroviral management of pregnant women is a major global issue since antiretroviral regimens offered to pregnant women to decrease mother-to-child transmission in many countries are often not highly active against HIV. The subsequent emergence of resistant virus can have long-term sequelae for the mother, child, and ultimately, other exposed individuals. The efficacy of antiretroviral therapy appears similar in men and women, although women may experience higher toxicity profiles, which may, in turn, be related to the higher antiretroviral concentrations shown in pharmacokinetic studies. Further investigation into gender-related issues, including sex-associated antiretroviral toxicities, unique pharmacokinetic profiles and optimal antiretroviral management during pregnancy is needed.