Anal atresia is a congenital anomaly, the exact cause of which is not known and effective means of prevention are still lacking.
It is now thought that anal atresia may be linked to genetic factors and is also thought to be associated with viral infections in early pregnancy, exposure to harmful chemicals, environmental pollution and nutritional deficiencies. Avoiding infections during pregnancy, avoiding exposure to tobacco and avoiding exposure to chemicals may be helpful in reducing the incidence of the condition, and maternity testing and screening during pregnancy may also help with early diagnosis.