A diagnosis of Fetal Alcohol Syndrome is based in large part on the obvious physical manifestations that come with alcohol consumption during pregnancy. The reduced fetal weight, facial abnormalities, etc. are indicative of FAS and are significantly easier to diagnose than the internal effects which are also likely occuring at the same time.
Fetal Alcohol Effects or FAE are limited mostly to the internal effects on the central nervous system and specifically the brain without some of the external indications of FAS. Sometimes this is due to less significant alcohol consumption or other factors that have limited the effects to the brain or other central nervous system functions without affecting the fetus in physically obvious ways.