An 8-month-old infant with cyanotic heart disease and transfusion-associated Babesia microti infection is reported here. At initial presentation, she was ill appearing, febrile and cyanotic. Laboratory tests revealed severe anemia, thrombocytopenia and an increase in hepatic enzymes. The diagnosis was made by the presence of intraerythrocytic parasites on thin blood smear and confirmed by serology and polymerase chain reaction. The infant was treated successfully with a combination of oral azithromycin and atovaquone. This combination is an alternative to clindamycin and quinine for the treatment of children with babesiosis.