Atovaquone has been assigned to pregnancy category C. Animal studies have revealed evidence of increased resorption and fetal harm; it is unclear if these effects were due to direct embryotoxicity and fetotoxicity or secondary to maternal toxicity. There are no controlled data in human pregnancies. Atovaquone should only be given during pregnancy when benefit outweighs risk.

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There are no data on the excretion of atovaquone into human milk. In a rat study, atovaquone milk concentration was 30% of maternal plasma concentration. The manufacturer recommends that caution be used when administering atovaquone to nursing women. The U.S. Public Health Service Centers for Disease Control and Prevention advise HIV-infected women not to breast-feed to avoid postnatal transmission of HIV to a child who may not yet be infected.

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