Fetal Alcohol Syndrome and Fetal Alcohol Effects are similar diagnoses. FAS is a harsher diagnosis, with a studied criteria of physical and mental defects caused directly by the effect of alcohol on the pregnancy. FAE is considered when the range of Effects -- that is, the actual problems caused by the alcohol -- do not cover all or even most of the criteria needed to diagnose FAS.

Fetal Alcohol syndrome is caused when a pregnant mother consumes an excess -- defined by most doctors as "any" -- of alcohol during pregnancy. Humans can process and eliminate alcohol, albeit slowly and inefficiently, through the liver, but a developing child has no defenses for the alcohol, which is naturally toxic. A fetus is therefore more affected by drinking than the mother. Symptoms of FAS include deformities in bone structure, mental deficiencies, trouble concentrating, low body development, speech/learning/language disabilities, and eventual problems with hearing, sight, and coordination beyond normal aging. FAS is considered a strong candidate for future problems with physical health, even if they themselves do not drink.

Fetal Alcohol Effects are diagnosed when only a few of the FAS criteria are met. For example, a pregnant mother might not know she is pregnant and so might drink, but then stop when she finds out. In this case, there might be a small amount of effect from the drinking, but not enough to diagnose full FAS. If the baby is born with facial deformities, but has no trouble learning, this would result in a diagnosis of FAE rather than FAS. One or more of the criteria might also be used to diagnose when there is no record of drinking, such as in the case of abandoned or adopted children. Generally speaking, FAE is a more treatable diagnosis, while FAS is more severe and harder to treat.