Babesia is a single celled protozoan parasite which may be transmitted through the bite of an infected tick, blood transfusion and/ or maternal-fetal transmission. We describe the case of a woman previously treated for Lyme disease and babesiosis who relapsed with severe malaria-like symptoms during the 3rd trimester of two consecutive pregnancies. Testing for active babesiosis was positive in both pregnancies despite prior conventional therapies, and she was subsequently treated with high dose atovaquone (1500 mg PO BID) and Zithromax during each of her 3rd trimesters, along with clindamycin during her 3rd pregnancy. At term, neonates were healthy with no clinical evidence of active babesiosis (no fever, acute respiratory distress syndrome [ARDS], hepatosplenomegaly or jaundice) and no laboratory evidence of babesiosis (no positive blood smears, hemolytic anemia, neutropenia or thrombocytopenia). Intramuscular benzathine penicillin was simultaneously used throughout her four pregnancies to prevent transmission of Borrelia burgdorferi, the agent of Lyme disease, with no evidence of transmission of the spirochete to the fetuses. Although this novel Lyme and Babesia therapy was effective in preventing congenital transmission of Borrelia burgdorferi and Babesia microti in consecutive pregnancies, future studies are needed to define the optimal management strategy for pregnant patients with Lyme disease and babesiosis due to the possible relapsing, remitting nature of the disease and the potential for associated morbidity and mortality.