Alcohol ingestion during pregnancy can be damaging to embryonic and fetal development. A specific pattern of malformation, identified as Fetal alcohol syndrome, has been documented in 1~2 of every 1,000 live infant births Fetal alcohol syndrome is characterized by growth deficiency, facial abnormalities, cardiac defects, minor joint and limb abnormalities, as well as central nervous system dysfunction, including microcephaly, mental retardation and abnormal neurobehavioral development. However, there are few reports of fetal alcohol syndrome associated with hormonal abnormality or amenorrhea. Recently, a case of secondary amenorrhea, which developed in a 19-year-old woman with fetal alcohol syndrome, was experienced at our institute, but the exact cause of the amenorrhea was difficulty to find. Herein, this case is reported, with a review of the literature.