Intestinal protozoan disease diagnosed in pregnancy is mostly controlled by symptomatic treatment. Specific therapy can be delayed until after delivery. Only severe cases, i.e. continued diarrhea leading to malnutrition of either mother or fetus, require an immediate specific drug therapy, which might be harmful to the fetus due to toxic and teratogenic potentials. Vertical transmission of intestinal protozoa has not been described. Invasive protozoan infections can be lethal to the mother making immediate drug therapy mandatory, even if the potentials of fetotoxicity or teratogenicity are known. Vertical transmission occurs independent of maternal symptoms, causing clinical disease in the child either directly after birth or during the first months of life. The knowledge of endemic regions and of the maternal travel history is essential for early diagnosis and treatment of protozoan disease in pregnancy and of congenital protozoan infections.