Twin pregnancy following assisted reproductive technology with a euploid fetus and a coexisting aneuploid co-twin constitutes a conflicting situation; therefore, it is important for the genetic constitution of each co-twin to be diagnosed accurately and promptly for parental genetic counseling and subsequent aggressive management. A 35-year-old woman, gravida 1, with a 2-year history of infertility, presented bilateral fallopian tubal obstruction at her infertility workups, for which she received in vitro fertilization; subsequently she conceived a twin pregnancy. She underwent genetic amniocentesis at 16 weeks' gestation, as indicated by an advanced maternal age. Presented with the diagnosis of twin pregnancy with discordancy for trisomy 21, a rapid fluorescence in situ hybridization (FISH) technique for aneuploidy mapping was applied for subsequent abdominal selective fetal reduction. The FISH technique facilitates the rapid analysis of uncultured amniocytes. Normal (disomic) and trisomic samples can be distinguished clearly and rapidly for subsequent selective fetocide. The FISH technique is an important tool in prenatal diagnosis and clinical applications.