Objective To survey birth defects of neonates conceived by using various types of in vitro fertilization and embryo transfer (IVF-ET) between 1998 and 2007 in Shanghai. Methods From 1998 to 2007, 8507 neonates from 6551 pregnancies conceived through assistant reproductive technology (ART) from 7 reproductive medicine center in Shanghai were enrolled in this retrospective study, including Shanghai Ji-Ai Genetics and IVF Institute, Shanghai Jiaotong University School of Medicine affiliated Renji Hospital,Buijin Hospital, China Welfare Institute International Maternal and Infant Health Hospital, Shanghai First Maternity and Infant Health Hospital, Shanghai the Ninth People's Hospital and the Second Military Medical University affiliated Changhal Hospital. The clinical data about the type and incidence of birth defect were analyzed. Meanwhile, the factors associated with birth defect were investigated, such as various ART,gender, mother age, numbers of gestational sac, the source and quality of sperm. Results The birth defect rate was 1.08% (92/8507) and the most remarkable malformation occurred in circulation system [34% (31/92)]. The rates of major congenital malformations were 1.21% (34/2799) in fresh conventional IVF-ET, 1.07% (20/1871) in IVF-frozen-thawed embryo transfer(IVF-FET), 1.04% (23/2212) in fresh intracyto plasmic sperm injection (ICSI)-ET and 0.92% (15/1625) in ICSI-FET, which did not show statistical difference (P>0.05). There was also no significantly different incidence of malformations between 1.12% (49/4371) in male neonates and 1.02% (42/4136) in female neonates (P >0.05).However, the occurrence of congenital malformation is positively related with maternal age, the rates were 0.84% (41/4884) in mother's age less than 30 years and 1.77% (16/902) in mother' age more than 35 years, which reached statistical difference (P < 0.05). It also showed remarkable different incidence among 0.53% (25/4679) in singletons, 1.59% (57/3576) in twins and 3.97% (10/252) in triplets (P< 0.05). No remarkable difference of malformation rate among sperm sources used in fertilization were observed, including 1.09% (81/7419)in ejaculated sperm, 1.21% (7/579)in percutaneous epididymal aspiration (PESA) and 0. 79% (4/509) in donor sperm (P>0.05). Conclusions The overall incidence of birth defect in neonates from ART is similar to those conceived naturally and is not associated with different types of IVF-ET, embryo cryopreservation, sperm sources. However, maternal age and multiple pregnancies coder the higher possibility of birth defect.