Objective To investigate the incidence of and clinical factors influencing neonatal birth defects from different assisted reproductive technology. Methods Between October 1998 and December 2006,1271 newborns from mothers treated by in vitro fertilization techniques [ including in vitro fertilization (IVF), intracytoplasmic sperm injection (1CSI) and thaw embryo transfer (Thaw-ET) ] matched with 269 newborns from mothers treated by artificial insemination were enrolled in Reproductive Medicine Center in First Hospital Affiliated to Zhengzhou University. Their medical information was analyzed retrospectively to compared neonatal characteristics, the incidence of birth defect and anomalous organs involved between in vitro fertilization group and artificial insemination group. Results In group of in vitro fertilization, those newborns with low birth weight from IVF, ICSI and Thaw-ET were 20. 0% ( 134/671 ), 22. 4% (92/410), 18.9% (36/190)respectively, which were more than 11.5% (31/269) cases in group of artifical semination with statistical significance (P < 0. 05 ). The rates of multiple pregnancy of 23.8% ( 160/671 ), 25.4% (104/410) ,21.1% (40/190) in subgroup of 1VF, ICSI and Thaw-ET were significantly higher than 10. 0% ( 27/269 ) in group of artifical insemination( P < 0. 05 ). The rate of macrosomia in group of in vitro fertilization was significantly lower than that of artificial insemination group (3.9% vs 8. 2%, P <0.05). However, the incidence of birth defect involved in various organs did not show significant difference between two groups ( P>0.05 ). Conclusions The incidence of multiple pregnancy demonstrated obviously increasing trends born with various In Vitro Fertilization techniques, which pave the way to high risk pregnancy. However, the incidence of newborn birth defect was not increased significantly. Thus, to lower occurrence of multiple pregnancy was the key approach to obtain neonates health.