This chapter discusses the implications of assisted reproductive technology (ART) in formation of congenital anomalies. Examples of congenital anomalies with ART include anencephaly, spina bifida, cardiovascular defects, orofacial clefts, and alimentary tract atresia. Imprinting disorders examined with regard to in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) conception are Angelman syndrome and Beckwith-Wiedemann syndrome, and recent reports have suggested a higher risk of these specific disorders after ART. Women receiving IVF treatment face a twentyfold increased risk of twins and a 400-fold increased risk of higher order births. Preimplantation genetic diagnosis (PGD) is ever evolving with fluorescent in situ hybridization (FISH) for sexing, aneuploidy screening, and structural chromosomal abnormalities and fluorescent and multiplex PCR as the most recent developments for monogenic diseases. Infertility itself is likely to be an important factor in congenital anomalies after ART.